First off, two old bugs seem to have toned down but are still around. Particularly related to traversing through rubble in decrepit buildings and map generation still being wonky. (Houses with invisible unopenable doors in Hamlyn, different textures in Hamlyn houses, trees spanwed inside of houses at Hold, etc.) This is from countless restarts. Most of these are reproducible and I can provide recordings and/or screencaps if it helps =-)
-Day/Night Cycle doesn't transition properly (some days last until 11:00 PM to 2:00 AM, then it's stuck at dawn until morning)
-The Free Stew quest\event is bugged. NPCs rarely spawn - usually there is just a floating chef's hat (regardless of time)
-The quest where you get the three gold records for the pawnbroker is broken (this is likely related to the newly implemented barter system. NPC says nothing about quest and gives no reward upon completion).
-Simon Says might need the damage decreased - At full sprint, was unable to complete without the rubber suit
-Some Quest NPCs are unresponsive - can be triggered by aggression with other NPCs in the area or some bugged NPCS (sick wastrel, for example)
-NPC Spawn rates in Hamlyn are off - it's not unusual for there to be groups of 15-20 clumped together in Hamlyn (might just be bad patrols?)
-House of curiosities consistently breaks. Sometimes no NPCs will spawn, except for the dancers/fetish peepshows(? Dunno want to call them LOL)
-Being in any of the time sensitive locations (e.g. only can be entered at night) will cause NPC's to despawn if you hide/sleep there until day.
-FARADAY! (Often she doesn't spawn in her room,in all of my successful full runs, she is spawned in the floor).
That's off the top of my head. I'll start collecting more in dept details - and start recording the reproducible ones if it helps.