The procedural generation of enemies isn't too difficult to achieve if there's only a certain amount of mutators. Even ones in response to player actions. Especially if there's a few enemy factions to fight, as it can "characterize" them in different playthroughs.
Using a lot of rockets launchers and HE autocannons? There'll probably end up being a higher weighting towards anti-explosive mods, to hopefully get you to try out some new weapons and to ensure you don't just stagnate in tech. In oldCom, lasers were fine, and you could go through a lot of the game with just them. So were plasmas though. The thing is, there wasn't really anything pushing you from one to the other, even though it was an upgrade.
If there's the ability to gain knowledge of various factions, then you'd want different loadouts against different types, and maybe even the need to bring along different specialists to use against each faction. I hope it doesn't end up as just some extra micro management for you though. Also, there's always the chance that the answer to anti-rocket launcher troops is to just take more rocket launchers, but this isn't necessarily a bad thing.
I also hope enemies don't devolve, and aren't always evolving in response to player actions (portraying the aliens/cthuluians trying new stuff out). This will allow for some stranger paths to open up for enemies, no matter your preferred playstyle, even if they don't seem to be paying off for a while. Slightly faster moving crysalids might not end up dying too differently than normal ones, AoE melee ones, super killy melee ones, or slightly more bullet resistant ones (just as you've moved to laser or plasma). But if it would set them on a path of fast->faster->flying->teleporting->"oh crap, how did that happen?" evolution, with plenty of other branches and random bits along the way, then the first two evolutions might not change much in death rate, the last two would be horribly scary. But it wouldn't be apparent that it's *that* much more powerful until the last two, so I hope the AI can still experiment with these things, regardless of player actions.
If different evolutions of different creatures were loyal to different factions, then you could try and pick your battles a bit. If they're the faction with super heavy armoured crabs, no worries for you you've still got some old AC and HC laying around that you could upgrade the AP ammo of a bit. If they're the faction with flying, teleporting crysalids and psi-floaters, they might be the "nope, not risking it" faction if you've got nothing to handle that.
It'd let each playthrough feel a bit more special in its own way, on top of the maps and missions.