Great game! There are a few issues though. I realize that none of these are easy to fix - they're just here if you're looking for improvements.
1. Let me close the pause menu with the space bar, the same way I opened it. I tried that every single time I checked the map or whatever.
2. In the same vein, can you keep the menu on the same tab when you open the menu as the last time you closed it?
3. There's just too much going on on the screen. Dragging things around behind you is adorable, but I mistake them for enemies every time, considering the number of flying enemies that jump you when you walk in 80% of the doors.
4. Also, the speech boxes and quest notifications block me from seeing a major portion of the screen. If you can make them more transparent, especially when I mouse over them, it would be a huge help.
5. Have a restart button (suicide) for the individual rooms - I got stuck a few times and having to reload the page becomes a pain.
I only do this because I care.
The achievement box is sort of big. One time it came up and covered my ship for a few seconds and I lost like half my life. Maybe either make it semitransparent or reduce the playable screen area to make an area where that kind of stuff shows up.