I'm fairly surprised no-one else has suggested this one yet, but it would be awesome to have some way to board and capture enemy ships. The easiest way to do it would be to have a component like an Assault Pod Bay that would be used like a Fighter Bay in combat. Chance of capture could be based on ship class and/or Infantry stats once ground combat gets squared away. It would make space pirating much more viable and give some good benefits to most aspects of D.I.M.E., particularly the Intelligence, Military and Economics. Diplomats could use captured Commanders like hostages in negotiations. Intelligence players could gain access to enemy fleet Intel, base locations, communication controls, etc., or use the ship for false flag operations or sneak attacks. Military players could make use of back-engineering to gain access to new technologies (as could Intel players) or just have free ships to add to their fleet. Economic players could sell captured resources, components or even whole ships (might make the market a more interesting place).
So there's my bright idea for the day, have fun with it!