First of all, I've been playing this game quite a lot, getting to the developmental dead end in the story several times with different builds, and it's far from my first time alpha/beta testing, and I've been playing these games since the early 90s.
I'll start with a topic that's dear to me: Crafting.
The crafting system in underrail is quite frankly somewhat annoying and could do with some improvement. It's often very hard to get the components you need to make what you want, and usually requires lots and lots of savescumming. This is caused by a combination of the item quality system, and limited, random vendor inventories. I've taken to doing lots of export/import when I start a new character to deal with this by stocking up from the start, to guarantee I can build the items I want... this process takes 2-3 hours. It's not ideal, and I'd rather not need to do this.
There's two ways to reduce the frustrations of the crafting system, one is quick and dirty, easy to implement, the other is more elegant but requires more work.
1) Increase vendor inventory sizes, and make them easy to refresh, such as by exit/re-enter the room/zone they are in. This at least speeds up the part scrounging process.
2) Instead of having different quality parts determine the quality of the resulting item, have all parts be fixed quality, but make the item quality depend on player skill(IE: automatically be the best quality you are able to craft). This is the more elegant solution.
Also it would be nice if the Galvanic Vest component were made available, and I'd really like a recepie for turning leather into carrier vests, especially since I'd like to have mutant dog leather carrier vests to make tactical/riot armor with acid protection.
I've also noticed that the new goggle lenses Ezra sell are all rock-bottom quality, leading to crappy crafted goggles, seems like you forgot to make them vary in quality, I did get some from Gort or Colton that scaled though.
EDIT: Also it bugs me a bit that there's no optional parts to put in the optional slots for energy/chemical pistols. At least allow lasert sight for the slot, please? I understand the game is far from finished, but hey.
Next up: Combat/Enemies
The most unfair enemy in the game is probably the bog standard Dog. Tackle stacking can get really out of hand very very quickly, effectively neutering your ability to do anything, especially when they come in packs. There's very little you can do about it if you're unable to kill them before they reach you(such as with a grenade, assuming you hit perfectly). I suggest a hardcap on Tackle stacking, preferably no higher than 2, or 3 at the outmost.
Second most unfair is anything that uses poison, again stacking is a problem, and of course the total armor ignore, and the cooldown on health hypos and antidote mean you can't keep up in an extended fight. Deadliest enemies by raw damage output, and often tricky to deal with(tough to kill burrowers, poison dart crossbow users with melee buddies, particularly sledgehammer guys that are a priority kill, giving the crossbow user more time to work you over). Poison attacks should probably not ignore armor, only the DoT effect should(and it shouldn't be applied if the damage was stoped by armor), and you may want to cap poison stacks as well.
Third: Travel
Backtracking manually through several empty screens is boring and a waste of the player's time, especially when it includes things like the infection scan at the cave entry/exit. Be nice to your players, don't waste their time with long boring walks, add a fast travel option.
Fourth, sidenote: Do you need some pixel art? I'm a pixelartist and I've among other things created mods for Dungeons of Dredmor(the hitchhiker's guide to the galaxy, hermetic gadgetry, circus freak, mutant, crafter's helper, and swedish food mods).
I'd certainly be able to whip up some item icons for you in short order, just give me a list(not too long, I have a full time job, but I could certainly provide a couple of dozen icons).