Do you see a chance to implement a mode, where FTL opens in window mode, but without borders, in the left top corner of the screen (my windows resolution is 1280x720, so it would be visually the same as fullscreen)? XCOM has exactly this mode and works very well via Splashtop.
And if you guys have to much time, I would really love to see FTL as a Windows 8 App with full touch control.