I'd change the 3 ability slots for a universal deus ex style 'hotbar' thing, which you can also use to drink potions and swap weapons without needing to go into the inventory. The controller equivalent would be a pop up radial menu.
Seeing other enemies attack and move in all directions makes me want independent moving/aiming with the mouse or other analog stick even more. but im guessing you want to keep it retro. This is why I'm not a fan overall, even though I really like the art style and ambition, the combat and movement just feels dated and unfun to me
other small stuff:
spending time breaking empty boxes is boring, either make them all have something inside and have less boxes, and/or make them break quicker.
it'd be nice to see what you just picked up in a sack as a notification
R should be able to close the inventory no matter what you're doing in it. The ability keys could also be used to quickly assign abilities.