The only major issue I have is using a 16:10 aspect ratio monitor, the UI is cut off for some things on the left and right side of the screen. It seems the game is made for 16:9 aspect ratio monitors and doesn't handle other aspect ratios well.
I have also experienced some major FPS slowdown when entering new areas, but it seems to go back to normal after 10 seconds or so, and doesn't happen on every new area.
Over all, this is shaping up to be a decent game with a good gameplay loop and nice progress on new versions.