Menus (e.g., the confirm changes prompt, start new game) should not touch the edges of the screen. The main character blends into the environment too much; normally you want them to be the opposite color from the BG. Pressing "Quit" from the menu needs a confirmation prompt. Run should be enabled by default or be a toggle. Settings menu should only ask for confirmation if you changed something. The mouse hitbox for that prompt is messed up. You should avoid obscuring the character behind foreground objects. Mixed resolution assets do not look good. Why is there no button to access the inventory directly? There also seems to be no "back" button for those menus. Pressing M twice backs out of the map menu, but not the note menu. Spacebar should be used to advance text in addition to E (I think it does sometimes?). I got stuck and quit after getting the BlastCaster, since the game does an awful job explaining how to use it. Most of the tutorials are bad; pausing the screen and forcing the player to read several pages of text is not a good teaching method. It make the game feel very intimidating to learn. Also I'm repeating the need for an auto-run option - moving feels like absolute ass without it.
The atmosphere is great, and it has a lot of effort and soul. it needs a lot of work in the user experience department.