Huh, apparently I haven't replied here beck then.
Here it goes:
"use of lighting"
In what respect? If you mean SS2 simply wasn't dark enough in areas where it may have been beneficial from a gameplay aspect, then I'd agree, but SS1 was the same except for deck 3 if I recall. If you mean SS2 was too bright in general and rooms/corridors too often appeared uniformly lit, again I'd agree, and again SS1 was the same. You get multiple ways to amplify lighting in SS1, yet it is only needed on deck 3. This gives me an idea: maybe one of the groves in the SS1 remake should be lacking lighting. That'd add meaningful diversity and shake up the gameplay, which I think is needed as my memory of the individual groves is blurred into one and the headlamp and other methods of light amplification see little use..
Even just deck 3 would be a pretty big exception, but there were also things like unlit alcoves with cyborg assassins on higher levels, darkened sections in R&D and whatnot.
The bottom line is that darkness and tools to mitigate it were both successfully used by SS1, but not by SS2 (basketball court with fritzed fuse doesn't really count and you didn't even get a shitty flashlight, while in SS1 you got lightamp, adjustable power flashlight and dermal patch that made you see in the dark).
"cybernetics"
Which SS2 cybernetics specifically? Implants? Yeah, unbalanced and not too exciting, though still more exciting than no implants.
Meanwhile SS1 had all manners of things you plugged into your jacked-up brain that did actual stuff instead of providing boring bonuses.
Stat bonuses are boring. If your game has a system for transcending mundane reality, being cybernetic augs, magic or enchantments, you should use it to achieve something you couldn't do by just pumping stats.
"explosives"
You'd like the ability to hand-throw grenades as in SS1 perhaps? I guess there was not really any reason to ditch that feature. Check out Secmod if you want it restored (can't vouch for how faithfully it was restored though, as I only used a hand grenade once).
Throw, fiddle around with timers, set up daisy chains of various explosives as traps or means to avoid thereof (like when blowing up computer nodes). Also the sheer variety of explosives. Finally, EMP grenades looked much cooler in SS1.
"puzzles"
I found them to be of similar quality, only unfortunately SS2 had less. Passcode in the art terminals, the missile jumping puzzle, and the red annelid egg hunting I guess can count as one too. I enjoyed these just as much as SS1's deck 4 force bridge puzzle, the reactor bomb segment, the retinal scanner requiring a specific severed head etc, though the latter I don't recall being too logical as all severed heads looked exactly the same, so you have to go by the location the head is found? May just be my memory failing me though.
I meant more along the lines of minigame based puzzles - SS1 wiring and circuit tweaking was more diverse than SS2's near identical hack/repair/modify minigames.
Proper, gameplay based puzzles were similar, I guess.
"Level connectivity"
Hmm. Well SS1's probably made more a bit more sense from a realism standpoint, as it is more interconnected overall and has more than one bloody elevator shaft connecting the first 6 decks, but aside from that both were decent to great.
Not shitting on SS2 here, but individual SS1 levels were generally more connected and complex.
"damage system, weapons"
While SS2's are flawed, SS1 has some things that are flawed in that regard too, or not necessarily flawed, but I simply don't like them:
First half of the game's weapons are completely outclassed by the second half. None of the ammo used by the first set of weapons is used by the second set. First half of the weapon set becomes utterly irrelevant, meaning all that ammo scavenging and tactical hording was futile, except for better outcomes for the player in the first half of the game. And what if I like a weapon from the first set and decide to keep it? I'd be gimping myself.
OTOH SS2 damage system was predicated on a misguided desire for symmetry between different types of targets, obviating such notions as hardened targets, and in the long run wrecking weapon balance.
Whatever problems SS1 had with its weapons, it didn't have nearly as atrocious weapon balance as SS2.
As for the RPG systems restricting you from even equipping a gun in SS2, this has its benefits. If we could use any gun regardless of skill in combination with the ability to pick up and drop weapons as we please, we'd have access to the 16 or so weapons + their ammo pool and be a walking tank, proving you leave all guns by the elevator and switch them out when needed. Plus this restriction enforces meaningful C&C, playstyle diversity and subsequently bolsters replayability.
The walking tank issue would have been a problem in SS1 too if the game starved you of ammo as SS2 did, but as it stands you never really feel you have to employ strategics with ammo conservation providing you explore, which is questionable.
Whatever benefits it had, were secondary to the fact that anything that makes you think "THIS IS SUCH FUCKING BULLSHIT!" has no place in a fucking immersive survival horror, because that's the only thing SS2 successfully was:
it wasn't a good RPG, it wasn't all that good FPS and it was a pretty shitty Sci-Fi story as well, being predicated on a station module jettisoned in Sol system mysteriously crashing on Tau Ceti V decades later in a setting with no workable FTL until after the crash.
It was just so fucking ace at making you feel alone, vulnerable and mildly mindfucked on spaceship swarming with scary aliens, alien-zombies and an occasional alien-zombie-cyborg that it became a timeless classic.
And in an immersive anything grunt being unable to pick up and fire a basic firearm is just plain fucking wrong. No matter what you should be able to fire most, if not all of the weapons, reload them, and deal roughly the same damage in the process.
As for replayability, SS2 weapon skills damaged playability before any re- could be applied to it. Narrowly specialized weapons are not a bad thing in an FPS - provided you are not forced to choose between narrowly specialized weapons and really good generalist ones.
There is nothing inherently wrong with SFG, fusion cannon, EMP rifle or exotics in SS2. They would all be viable and fun to use even besides the almighty AR *IF* they didn't have to compete with it, each other and all kinds of useful skills for valuable cybermodules.
With skill system included there is little point taking max research AND max exotic to get weapon that can't even scratch half of in-game enemies, including final boss, if you can just blow everything away with AR for less than half the cost (AR is relatively easy to maintain, for example).
Weapon skills could have worked well if they instead tweaked parameters like reload time, jamming frequency, degradation rate and ability to maintain weapons of given type. A character unskilled in standard weapons could then keep an AR as powerful, but unreliable backup with use limited by durability rather than ammo which would still create different playstyle than popping everything with AR, even if lugging mostly dead-weight around would be attractive in the first place.
Viability of lugging around different weapons could also be limited by having limited ammo stack sizes (don't forget that SS1, in addition to general abundance, had hammerspace ammo and no durability system).
