-One thing I would suggest is making Capital ships incredibly hard to kill with normal weapons, giving a higher fire-rate on the weapons so they're better at tracking fighters but slowing them down to a crawl. Then having torpedoes which are ridiculously powerful as the primary way of destroying capital ships. Can be balanced so they don't work very well against fighters by giving them a tiny turning speed. Also removing the level 10 missile slots from normal fighters so only bombers can mount the torpedoes, then make the bombers very slow at turning so that fighters can out-manoeuvre them and don't have to joust and therefore reduce their risk of being hit by torpedoes.
Create rock+paper+scissors tactical combat, IE Battleships beat Fighters, Fighters beat Bombers and Bombers beat Battleships. Because to me (admittedly I haven't played the mod very long so correct me if I'm wrong) it just seems like right now it's about who has the biggest rock, not the best tactics. Capital ships would obviously be very powerful generally in this balance, so it would be wise to make them very expensive. So expensive that battleships are actually rare and that only clans with a lot of financial power can buy them.
-I have a feeling this has been drudged many times before but the ability to dock in player controlled battleships would be uber-cool, dunno if it's possible in the engine or not though.
-Remove the Titan NPC's from Corsair missions. There's something not quite right about their model, I can often fire all my coalition capital guns at them for several seconds and despite the fact I've filled them with enough laser to kill them 3 times they can fly away undamaged. I don't have those problems with the other Corsair or Outcast spawns so it seems to be limited to just Titans.
Can't think of anything else right now.