Hmm- hiding in space? How about allowing ships to hide in orbit around system bodies- basically shut down with minimal life support, so there's a chance to be detected, but it's greatly reduced.
I'd like to see better AI and more ability to use tactics/maneuvering in combat. For example, parking some gunboats in among the asteroids, while your main fleet "falls back" from the approaching enemy craft- then, at the appropriate time, the gunboats power up and fall in behind the enemy, who's got a limited rear firing arc, and greatly reduced sensors from the rear due to interference from the engine's wash...
If anyone's played Battlefleet Gothic (a tabletop game in the WH 40k line) some of the ideas in there might be useful- fire arcs, using gravity wells to turn, etc. I think the rules are available online for free now if you look. Oh, it also deals a bit with Newtonian momentum, but I don't know how much of that you're planning on using in this game.