Here's a thread for things which aren't necessarily bugs (or even are) which would be very nice to see patched in the base game.
-- Ingres' teeth involuntary shapeshifting.
When you make them magical or improve their magicness they revert to crushing damage. If you don't know this, you're stuck with morte doing crushing damage which you probably don't want. If you DO know this you have to click them again to change them to piercing.
-- Abishai respawn "off screen".
When you kill Black Abishai in the Hive, many of them respawn quite a bit off the edge of the map. Many times you can't even see them, maybe just the edge of it's foot, and they're deep into the "click to leave map" area. It'd be very nice if these guys respawned where they ussually spawn, in the proper walking area, like thugs do.
EDIT: More in-depth: the new "autoloot" feautre obscures the bottom edge of the screen even when fully zoomed out, and that's where 3 of the 5 Abishai respawn (and often get stuck), so you can't even see them if it's turned on.
-- Being able to sell multiple Cranium Rat tails at once
Really. Having to click through huge stacks of them one by one if you want to sell them is a pain. Making Phineas T. Lort in the office of vermin control have dialogue options for getting rid of 5, 10, 20, 50 depending on how many you have in your inventory would be a big QoL improvement in this regard.
-- Journal/Quest entry for finding out about the Decanter of Endless Water
When you solve the quest you got from Glyve, the Face in the Stone in the catacombs, one to bring him the decanter of Endless Water, he then tells you to seek Nemelle for the command word. This doesn't get a journal or quest entry, and it kinda should.
-- Some disambiguation between Dirty Rat Charms and Cranium Rat Tails
One of the many confusing things for new players, and PST always has them, is that Dirty Rat Charm and Cranium Rat Tail look exactly the same. If anything at all could be used for the graphics of the Dirty Rat Charm it'd be very nice. Even just rotating the same image or mirroring it left to right, or anything.
It's all further complicated by people asking for Cranium Rat tails and there being a Cranium Rat Charm which isn't what the people are looking for.