Research facilities: These are still an absolute mess.
I still think that the spawning mechanic simply doesnt work. There's way, way too many enemies in the game that need a careful approach to defeat. You can die here ENTIRELY because of what the RNG does, and there's little you can do about it. Run & gun just does not work in this game, and you cant simply avoid everything either.
Heck, I cant remember the last time I cleared one of these WITHOUT just dropping the difficulty to nothing. I'll usually TRY them a couple of times on Hero, but literally every single one, I end up just dropping it and essentially skipping them, because there's no other solution.
Currently, I see these as pretty much THE screwed up part of the game. The fact that their danger level is often super-dramatically higher than..... everywhere else, also doesnt help. But even without that, these would still often be utterly unbeatable.
In the one I just did, I exited the hacking room to instantly run into 3 of those robot fish, 2 of the super-long-range spider crawlers, 2 scouts, a floating thing with rockets, and those rolling guys with the splitting shots from the abandoned towns. There was no quick way past here without getting hit by EVERYTHING, but I cant do it carefully because that spinning whatsit keeps farting more monsters at me.
Another one occurs to me: Level-up towers, I'd say, stop these from randomizing the enemy selection. Leads to ALOT of frustration. In pretty much any other area of the game, when you run into a nasty situation, you can leave the area, and switch mage classes and perks in order to deal with it. But not in these. When you go back.... chances are all of the monsters are different. Preparations simply dont matter in these.
Certain types of monsters should also probably be disallowed here, particularly melee-only types. (EDIT: Or not. It took me awhile to notice just how the melee stuff was working now. A good change! Though I still think certain monsters probably shouldnt appear here.)
EDIT 2: Also, having areas reset when you re-enter them, instead of having every monster be exactly where it was, would be a good idea. Some areas can become completely unbeatable if you screw up in a certain way, meaning that the only way to deal with it is to restart the game, or even delete the file containing that particular tile so it regenerates. Had this one happen just now.... blasted seeker spell, instead of targeting any of the 4 enemies that were somewhat near me, targeted the thing that was furthest away, which was one of those horrible imp blobs, whatever they're called. So now there's 4 of those horrible things just sitting on the entrance to that surface area.