How about some sort of defensive facilities for planets? Something that you can upgrade like a factory, but instead it boosts the power of ships in orbit. Maybe even prevent small fleets from taking planets (I would have a pretty high defense facility level to enemy ship ratio for this though, perhaps 2-3 levels to defeat 1 ship).
Fog (Nebula?) of War would be nice. Make it a little bit more of a surprise when you come across an enemy player's planets.
There really should be some more achievements that can only be acquired in Multiplayer. I got all but the "Perfect!" achievement in the first few hours of play. Perhaps something based on the number of human or AI players in the game? I remember an old computer game ad that showed a picture of a computer chip with the caption that said "This opponent is programed to be challenging". Then it showed a picture of a crazed looking man with the caption of "This opponent wants to rip your lungs out". That would be a good basis for a pair of achievements, IMO.
I haven't played too much with customization yet, so this might already be possible. How about an option to start each faction with multiple planets in clusters?
This idea is probably just the MoO2/GalCiv2 player in me talking, but what about random events that affect the entire map or maybe just one faction? Nothing game breaking, just minor things like a small bonus or penalty.
Thats all I can really think of in one sitting.