1. Add option to pause the game instantly after a jump Would just be kinda nice, you know.

2. Beam weapons show starting point and direction
3. When targeting a beam weapon, rooms affected are lit up as if targeted by regular weapons Might not be immediately clear why would you want this, but let me explain. When using beam weapons, you generally have another weapon to break down shields (unless you start with something like The Glaive). In some cases, you have 1 laser weapon and a beam. If I shoot my laser and it hits just shield layer so my beam can hit, I want to start my beam at the shields system. If the shields system is hit first, this will prevent it from regenerating in time and my beam will hit other rooms. Sometimes I happen to accidentally start the beam at the wrong side, don't realize it's targeted incorrectly and waste a lot of potential firepower.
The outline is just a thing that would maybe clear up some confusion, as you pretty much play Tetris when firing beams - you want to hit as many rooms to maximize damage, but sometimes you can hit the very edges of rooms and just hope it counts. By adding the outline, the confusion would be removed.
POTENTIALLY RADICAL AND ABSURDLY OVERPOWERED
I have a feeling bombs are a little underused at one point. Never have I feared bombs, never have I wished I had bombs, never have I thanked that I received bombs (exception would of course be the healing bomb when playing with a teleporter). They are not that great, to be honest - there's a chance you'll miss, unless the crew is guaranteed to die you will not make a very large impact (no pun intended) in the later game with them, and generally feel a little weak. My suggestion? Ability to target bombs per square or in between tiles instead of per room. Bomb blast radius - 4 tiles. Bomb blast radius
Gray lines in rooms indicate tiles
Opinions? Ideas?