"I hate to be a dick, but fact check: Calling GMDX a straight upgrade to vanilla is not accurate.
The reasons are long winded, but I'd break it down into 3 main issues: 1. Massive shifts in balance and considerable changes in design philosophy 2. Violations to canon, particularly in regard to technology. And 3. Unintended jank and bugs inserted into the game, even after its attempts to remove bugs are said and done.
Vanilla does have bugs and potential softlocks, but honestly its potential exploits are more of note, and even those are pretty slim. There is no explicit reason to need to overhaul Deus Ex in terms of function. Only its appearance and pacing tend to be dealbreaker for modern players. I would personally wager 95%+ of new players that walk into vanilla will not have any game-breaking bugs or massive setbacks from technical glitches in Deus Ex. I'm keeping this comment short, but I'll add one in reply to briefly skim over some of the issues GMDX presents, because the details may matter to some people, depending on their thoughts on particular aspects.
Anyways, blowing through these points one by one, I'll try and explain some of the gripes I've seen with it, having peeked under the hood a couple times, and generally having had technical experience and knowledge of deus ex above that of most people. I won't claim to be a god or the go to guy for anything, as that would be absurd. But I have played the game for 15 years and modded it for 11 in some shape or form, so I'd like to think that counts for at least something.
(1.) Shifts in balance and design philosophy: In regard to balance, weapons, enemies, and augmentations have seen dramatic changes.
For weapons, one of the most infamous examples is that of the standard pistol. The standard pistol is now capable of accepting a silencer, unlike in vanilla. This is absolutely catastrophic, in terms of impact, since the Stealth Pistol was always gated behind this key difference, with its considerable weaknesses in performance offset by its ability to be a lethal, direct-fire, pistol skill weapon. Now that the standard pistol can be silenced, the stealth pistol is now useless. I wish I was kidding on that note, but GMDX also increased the pistol's capacity from 6 to 8 rounds, doubled its rate of fire, and lowered the damage from 14 to 11, as somewhat of an offset. The stealth pistol, meanwhile, has had its rate of fire cut almost exactly in half, while also having its reload time doubled. Its capacity has jumped from 10 to 15 as well, but considering it's half its previous speed to deal damage, and half its previous speed to reload, that's worth piss-all at day's end, especially since it doesn't provide any benefit for ammo efficiency. Its damage is unchanged from its base number of 8, but its base accuracy has been raised 7.5%, on the plus side, giving it a mere 2.5% better accuracy than the pistol.
However, the problem with pistol vs stealth pistol can easily be summarized by the problem that, if you are a pistol main, you will always silence the normal pistol as your first silenced weapon. Once the normal pistol is silenced, its burst damage, damage per second, ammo efficiency, and reload time are all completely superior to the stealth pistol. Its single greatest limitation has been removed, and even when comparing the 2 weapons when fully modded, the standard pistol still reigns supreme, with it also having the advantage of being acquired sooner, and being easier to mod sooner.
There are 4. Four god damned pistol weapons in Deus Ex, including the disposable ps20, and 1 of those 4 has been made inferior to another of the 4 outright. There's some serious beef to be had there.
There are more weapon balance issues to be had, but that one speaks serious volumes.
Let's talk enemies. GMDX has often touted that lategame difficulty has been too easy. I would heavily argue this is veteran's bias, particularly around M15, since it relies strongly on ambushes and challenging enemy compositions, which are all ruined by the metagaming caused during replaying the game. I cannot find a single review anywhere citing lategame difficulty as an area of issue for Deus Ex around the time of release, and this was the very same year "John Romero's about to make you his bitch" was a selling point for Diakatana. Difficulty was something people frequently looked towards in game releases back then.
So, let's talk enemies. A particular animal I'll be referring to known as "G's" in this context, to reduce spoilers slightly, are known for having had 50 health in vanilla. They now have 250 in GMDX. Greasels, in vanilla, have 100, and karkians have 400 as the absolute piles of bricks they were intended to be. 250 is not inconsequential, especially considering G's were "glass cannon" enemies to start with, boasting a particularly strong native ability to kill you just by existing near you, without the need for attacks, while also having a shotgun ranged attacked. Everywhere G's were put in the game was specifically designed around their glass cannon nature, to make footwork and tactics key on the limited timeframe you have to fight them in close quarters. Quintupling health for these isn't merely "difficulty" tweaking, it's directly butting heads with how much space you can keep between you and these foes without dying because the game said so. Tactically, it's making the gameplay greatly risk committing suicide.
Greasels, on the topic, now have a leap attack, a melee attack, and fire 3x the amount of projectiles (now obscured by trail particles 3x in quantity and 10x their vanilla scaling, in case actually dodging wasn't a fair enough tactic), and 3x the swim speed they previously held. Additional greasels have been added to a few levels, but most notably this happens in the Ocean Lab, where there's lots of water. Bonus fun factoid: Testers bitched about the increased greasels in GMDX v9's Beta, but even after reducing the count since the Beta, GMDX still has 15 greasels in 14_OceanLab_Lab, whereas vanilla has 9. I have never to date talked with anyone about GMDX V9, including people who love it, who has not thought that the Ocean Lab's balance in GMDX is patently ridiculous across the board. Yes, that's anecdotal evidence, but there's math to back it up, too, so it's far from mere speculation in my book.
Meanwhile, Military Bots have rockets that deal 3x the damage in 4x the blast radius, sporting enough power to one-shot the player on any difficulty (including the extra baby mode GMDX made "easy" difficulty into, ironically because of the obtuse nature of the game's mechanics when digested by modern players), and can do so at an increased allowance, thanks to boosts to blast radius. Blast radius also affects how damage is dealt in Deus Ex, so it indirectly boosts damage, on top of the 3x bonus already given. Combined with the "suppressive fire" feature GMDX threw in across the board, this means Military Bots can kill the player easily in a straight fight, and can often easily kill the player anyways, even after they're attempting to use cover. In practical terms, this is a massive redesign in how the enemy operates, and shouldn't go unnoted.
MIB's now have Super MIB's later game, which use... Nanotech technology. Violation to canon I'll get into later, but suffice to say they have increased health, massive boosts to ground speed, and substantial resistances to key damage types.
A previous cut content enemy has been restored, the SecurityBot4. I'll spare you its colloquial nickname, and mere mention it has massively increased groundspeed vs vanilla's intended design for it, leaping from 95 to 220. That's just over double. It also cloaks (robots are never seen cloaking in vanilla, making this is a probable violation to canon), has rapid fire rocket pods (please kill me. The robot is the size of a minifridge and has rapidfire rockets? Have you seen how space consuming rockets are as a weapon type?), and can now climb up stairs and smash through solid metal doors.
On the topic of giving enemies rockets for no reason, large Spider Bots have been given machinegun rockets, too. Whytho. They're described as a Riot Control robot in the lore, and they now have rapid fire rockets that they have no storage medium for on their person. They also now fire grenades with extra mini spiderbots inside them, which are also not vanilla in how tiny they become. Yes, we see nanites in lore, but there's no reason to assume any type of bot can be come any size without any repercussions. So. Many. Canon. Violations.
On the topic of spiderbots, small spiderbots now have double the range for their electricity attack, and large spider bots have 1680 max range for their electricity, instead of 1280. The damage values for spiderbots have also gone from 40 and 13 (small version) to 30 and 18. Small spider bots are much more common than large spiderbots, though, and this electricity attack is noteworthy for being a huge pain in the ass in vanilla. It's a shotgun-esque, instant hit attack that can be fired from virtually and position or circumstance from the spiderbot, so doubling its range and adding some extra damage points goes a long way to illustrate how the original enemy design was problematically designed, while also just making it stronger to begin with. Also, small spiderbots now walk on ceilings in many instances, which is both annoying, and yet another violation to canon technology.
Let's talk augs.
For those who don't give a shit though, melee damage has been relocated into a mid-game aug, instead of a choice for the first aug, which is part of a long-spanning campaign GMDX wages early and mid game against being able to break doors with melee weapons... Which is a very intentional choice made available in vanilla. Not all breakable doors have been unbreakable early game, but an alarming number of them most certainly have. Some are buffed, most have just been accidentally buffed by relocating the availability of melee damage...
But fuck all that. What we should really talk about is the new muscle aug. Please. Kill me.
The new muscle augmentation, instead of offering bonus lifting strength and deco toss distance while active, at the cost of energy in real time, now operates totally different. It now costs no energy to lift a heavier-than-normal decoration over time, decorations can be "powerthrown" for 0 to 2 energy a toss (most notably, most decos cost nothing at all to powerthrow), often with enough power to kill an NPC in a single shot, if thrown right, and offer a number of passive bonuses for absolutely zero cost, including: Complete and total weight penalty negation for heavy weapons, extra throwing distance for inventory items (great, except for its tendency to now break things no matter what you do when dropping them), no longer dropping carried decorations when taking damage, and moving faster with carried corpses.
Wrapping up bullet point one, naked solutions to solutions have been eliminated in the majority of obstacles thrown at you in GMDX V9. Lasers that could be climbed over with the use of crates can no longer be climbed over (M02, M03, M04, M08). Areas you could previously walk through unopposed now have lasers blocking the path in question (M02, M03, M04, M06, M08, M15). The behavior of lasers has been modified to not allow for blocking lasers with decorations in most instances it previously worked (M09, M02, M06). TNT crates are vastly reduced in numbers (M09, M01). Doors that were previously not locked are now locked (M01, M05, M06, M14). Hell, many parkour solutions not involving lasers or other nonsense have still been deleted outright. (M01, M03, M06, M15)
(2.) Violations to Canon, particularly in regard to technology.
I already covered many of these in enemy balance. This is no coincidence. GMDX willfully tosses aside the technology and technological implications established in vanilla on a number of occasions, just so people who really like difficulty can get their rocks off.
Things that now violate the original canon: Computer hacking, extra mini spiderbots' size, SecurityBot4 across the board, super MIB's just freaking existing (nanoaugmentation is not technology we have any reason to believe is ready for use on goons), Radar Transparency vs laser tripwires, mini spiderbots' ceiling walking, GEP Gun laser/scope guidance, large spiderbots for damn near everything, and skills vs grenade blast radius.
I'm sure there's some I'm forgetting, but close enough. GMDX never tries to change how the story is told or anything as shameless as that, but it changes a lot of what is seen and experienced on its way to already departing from vanilla's design philosophy, making it double collateral. I could understand a mod taking some small liberties, like maybe those extra mini spiderbots or the computer nonsense, but stuff like the MIB's and Sec Bot 4's are just a slap in the face to Deus Ex's worldbuilding I cannot personally ignore.
(3.) Unintended jank and bugs:
This one's relatively swift, as bugs are cut and dry. TL;DR: (1.) Enemies now spawn fire extinguishers near the player when calculating grenade tosses. Yes. Seriously. It's old, unconventional debug code that was never removed (2.) Weapons can now spawn without ammo, due to changes in item collision (3.) Due to changes in physics, dropping decorations on pawn's heads can now cause the decoration to delete itself, if DeusExDecoration.Bump2 and ScriptedPawn.SupportActor are run in the same frame... Which is pretty damn common. (4.) Items can fail to drop or be spawned correctly, in a similar vein to ammo resupply issues. This is seen in some edge cases when items get dropped in 05_MJ12, very rarely deleting the player's items on accident. (5.) NPC's are programmed to drop their items when gibbed in GMDX. This is code copied and pasted from Human Renovation, and trust me, copy+pasting someone else's code is painfully common in GMDX's framework. NPC's never drop their items, though, due to yet more changes in item collision properties. Somehow, nobody ever noticed this extraordinarily obvious bug. (6.) Some kinds of new flesh fragments (FleshFragmentWall, I'm looking at you) can crash the game, due to oversights in the way the lifespan code is built (7.) Massive performance bottlenecks on now-Lowend PC's that could previously run vanilla very well. Long and drawn out 3d math is run on every single owned weapon every single frame of the game, even when it's owned by an NPC and its first person effects cannot be seen. (8.) Massive, massive amounts of Accessed Nones in the logs. Some players have reported logs spanning thousands of lines of these errors, because somebody didn't check their code, and the 3d math bottleneck listed below also has accessed nones in some weapons that can be ran multiple times every weapon, every frame. The log spam is an absolute catastrophe, and probably isn't helping performance either. (9.) UNATCO helmets are supposed to work 100% of the time and make the helmet fly off 8% of the time. Instead, they work 8% of the time and make the helmet fly off 100% of the time this happens. Oops. (10.) G's magically restore their now 5x as large health pool every time the game has its level re-loaded outside of hardcore mode, including on loading a save of that level. (11.) Other enemies have similar health/emp stat restores to what's listed above, but they're prettymuch all in Hardcore mode only. (12.) Muscle aug now has an exploit where you can spam left mouse with nothing in hand, and you'll never play the footstep frame on your run animation, thus letting you run without making noise. Oops. (13.) Many items on the ground that are activated with left mouse will produce different effects vs in-inventory usage. Candybars, as a random example, will heal 3 points instead of 2. Many items have issues of some sort, however. This one's great, because it's caused by redundantly trying to mirror what objects would do when they were used by the player normally... Instead of just making them do that, despite the fact it's 100% possible to do, and actually an easier method. (14.) Geometry errors. One geo error I know of is now solved in GMDX, while a fistful of other have snuck in instead. (15.) Snipers don't drop their sniper rifles like intended during death. (16.) If multiple alarms go off in a row, enemies in-level can gain infinite amounts of vision in darkness, seeing the player in any light condition, including perfect darkness. (17.) Gunther and Anna are supposed to be stunned by EMP grenades now. This feature has never worked in GMDX. (18.) Confix is credited as being added to the game, but all the bark content Confix restores doesn't work in GMDX, because ConBindEvents() was never called in the code. (19.) Snipers that strafe during "scoping in" scope in faster while strafing. That's right. Faster. (20.) Flamethrower flame thresholds seem to be janky, if not broken outright for some foes. (21.) Many enemies now make knock-out sounds instead of death sounds, even when killed by lethal means. This is bad audio feedback, and in fact, one enemy even makes laughing noises instead of large pain noises in v9. Check the riot cops near the Ton Hotel in M09, and you'll see the culprit in question. (22.) Using vision aug now makes the player visible to enemies in darkness. Oops. (23.) SecurityBot4's now routinely crash the game. Their AI type, combined with their unusually high ground speed for a robot, can cause them to overshoot when crossing AI nodes, creating a runaway loop. (24.) Hardcore mode is supposed to lower player accuracy by 10%, but never does, due to badly phrased code. (25.) PS20's now have their ammo appear in inventory as "DEFAULT AMMO NAME - REPORT THIS AS A BUG!", whereas they previously did not. (26.) There's at least one NPC weapon that isn't supposed to be attainable by the player, but if you gib the NPC at the right moment, you can get an assault gun that shoots LAM's as EMP grenade shells. (27.) The game will change your configuration settings for auto reload, crosshair visibility, and real time UI on you. 2 of those 3 are from playing in Hardcore mode, but 100% of them are preventable, and will save between game sessions. Kill me.
I'm sure I'm forgetting some, yet again, but those are the big ones.
Jank is a larger category, and I'd be here literally all day to try and get them all. Instead, here's some fun ones: (1.) Snipers cannot drop sniper rifles from arm damage. This is intended, but is a cheese mechanic done instead of increasing arm health. (2.) There's these super awful triggers in vents. If enemies are trying to attack you, but you're in a vent, and you step in the right spot, a gas grenade will magically spawn in front of your face and explode. Depending how the player moves, in relation to TouchLists in UE1, this could happen never, or it could spawn multiple gas grenades consecutively. (3.) Enemies that hear an alarm once will permanently gain ground speed. Their resulting speed often looks immersion breaking. (4.) Many of the balance issues already listed. Lemme save some time there. (5.) Shotguns can now be reloaded shell-by-shell, but you can't see your ammo counter while reloading, making tactically interrupting questionable. (6.) Mantling is horribly overpowered, and no matter what anyone may try to claim, it has not been accounted for properly. Some maps have less boxes to stack, so you don't climb out of level. Joke's on them, you can climb out of most levels anyways using mantling. I got on top of castle clinton and just started sniping everyone out of bounds one day. Greatest cheese I ever done seened. Other players have gotten on the walls in liberty, or in unreachable buildings in Paris, and used those for all sorts of hijinks. (7.) You can't die of smoking cigarettes when using real time UI. (8.) EMP grenades make your HUD invisible, but the intended method of restoring it is opening a pause menu and closing it to resume the game. The intended. Method. This is awful, and as a coder I can state for a fact it's sourced in making the hud disappear with a single, crappy line of code, instead of actually disappearing in a comprehensive manner.
I'm gonna stop there, but you get the point."