One thing I'd like to see is new ships/weapons, preferably with new models and with some thought put into why they're there. Also, a big pet peeve of mine is when someone makes a new weapon and names it almost the exact same as an existing weapon (examples: Subach HL-8, Prometheus Q, UD-9 Kayser II, etc). If there's a new weapon, it should have a different name.
Some other things:
1) Be realistic in your plot.
2) Don't spring too much new stuff on the player that hadn't shown up before because "it was classified". It can only go so far before it's cliche'd.
3) Don't overuse the Aeolus. Sure, it said only 24 were put into service, but more might have been made. Still, if the GTVA only got 24, and only 5 are unaccounted for from the main campaign, there shouldn't be that many Aeoluses at all.
4) In populated systems, don't forget the civilians. If nothing else, they can provide scenery. And, if a battle happens, they can just leave.
5) Don't be afraid to provide a little comic relief.
