[...] those Nightmare-crushing juggernauts are quickloading? If it's not very often: congrats, you really are good with these games![...]
Assuming you're talking about
the Nightmare and not the nightmare difficulty, the level of difficulty in dealing with them comes down to how you approach them. With Psychoshock, Firearms 2 (which I never aspired to take, I just ended up with so many neuromods that I practically had to max out Engineer/Scientist/Security because I didn't want to take more psionics) and an upgraded Shotgun, the Nightmare poses absolutely zero issue to anyone, even if you're a CoD-playing downie with average IQ of an australian aboriginal.
You simply get into a good position, Psychoshock the bastard so he can't throw psychic spergballs at you, simultaneously taking out a ton of his health, and then blasting him from as close as possible; the last 2-3 shots can easily be at point-blank, because he'll take so much damage he won't have time to actually attack you physically.
If you don't have those tools at your disposal, though, then yes, the Nightmare is fucking scary, and will tear you a new asshole and make you waste your ammo. The most important thing remains to shut down his ridiculously strong spergballs, though, since they home in on you and can pass through basically everything (which is incredibly unfair, considering that
your psychic abilities can't even pass through breakable glass) and that can be done with a Null Grenade.
I feel like that last point is a good idea: fabrication licenses would make an excellent exploration reward. What would be a better find, a license for 10 more neuromods, or 4 neuromods? Using licenses you can impose some limits on ammo, medkits, etc, and have a nice reward for exploration.
[...]
Yes, the beauty of licenses is that you can hand them out as meaningful rewards without ruining the resource economy, since the total amount of materials will still remain the same, making it possible to create an aspect of prioritization and a feeling of scarcity without it necessarily being debilitating by it's very nature (because you may run out of some licenses, but you'll likely have some others left).
I can see the complaints about the lack of difficulty for people who are experienced with this sort of game and don't take on enemy engagements like a dumbfuck Xbox player would, but let's not pretend that System Shock 2 or other games in the "immersive sim" genre that came out around the same time are hard at all even on Impossible difficulty. In that game you can have an endless supply of hypos of all types, never run out of ammo once you're out of the early game if you use the right ammo or right weapons on the appropriate enemies (3 shotting rumblers with a shotgun or instagibbing giant robots with the bugged grenade launcher in that game that gets a 100% damage increase upon upgrading it instead of 10%).
The only truly difficult games in the genre are Ultima Underworld 1+2 and System Shock 1 and much of that comes down to the controls (which are a non issue in SS1 Enhanced or mouse look mod) and also in SS1's case some of the later enemies being really cheap and just raping you with ranged attacks almost instantly, but I guess is still valid and forces the player to find ways to deal with those enemies. Shock games also have the single-player respawning gimmick that Prey lacks so that balances itself out if you're playing within the confines of the game without reloading a save every time you die.
I think that comparisons to SS2 are fairly irrelevant in this, honestly, and I don't think it's so much as issue of actual
difficulty as it has to do with the
feeling of oppression and difficulty. In terms of actual difficulty, you could likely play on Nightmare and get through the vast majority of the game with just a Wrench and sneaking, especially if you invest heavily in psionics, which is super-effective, resource-wise. Far more cost-effective than any weapon.
Pure "difficulty" is often just a matter of numbers inflation and eventual save-scumming. You could make every enemy one-hit you and the game would be more "difficult", but it wouldn't actually
improve anything. The feeling of difficulty lies in manipulating the player into feeling that things are difficult without encouraging them to simply reload when something goes wrong, and the best way to do that is really to make them
think that they can die at any moment, even though you actually rarely hit them with sledgehammer shots, and force them to manage their resources.
And real increases in difficulty involves adapting your playstyle and mastering the mechanics, optimizing available resources, not just making things more deadly or harder to kill.