I'd like to see more variety in the large scale objects in space, especially in a tactical way. For instance, i think it would be neat if, upon entering a star's "system" it's massive radiation would immediately start to damage a ship's shields. So it would be dangerous to pass through them as fleets hop around the screen.

Magnetic clouds/storms could temporarily knock out anti-matter on ships. The addition of black holes could be fun too. Say, if your ships get too close to it's gravity well, they get sucked in.

There could be stars having solar flares or other, perhaps random events that could make space travel more perilous or intresting in various ways.  I think it would be really neat if the status of planets changed after prolonged nuclear bombardment so that Terran planets could be redcued to a desert or ice or radiated status.

Any more ideas?