I'd really love an RPG style flagship upgrade element. Here's some ideas for upgrade lines, bearing in mind that I haven't played the game and thus some of it may not be relevant (the idea is that you wouldn't be able to get everything in a game, so you'd have to choose upgrades):
1. Carrier
- Increase ship deployment speed 10/20/30%
- Increase fleet repair speed between battles (by some amount)
- After battle, automatially replace 1 destroyed ship up to (fighter/small ship/medium ship) size
- Increase maximum fleet size
2. Diplomats
- Add propaganda specialist to your flagship, increasing bargaining points gained from combat victory
- Mercenary Contact - Can spend BP to add bonus merceary ships to your next combat
- Special Envoy - Create quarters on your flagship for an envoy from (1/2/3) races, granting a permanent relations boost. Once selected, the envoy choice cannot be changed
3. Combat (for those who want a more active flagship)
- Add long range missile launchers to your flagship, allowing it to deal direct damage in combat
- Add extra shield generators to your flagship, increasing its defense
- Convert 10/20/30% of hangar space on your flagship to combat quarters, greatly increasing offense and defense but reducing fleet size
- Fleet Shields - Once per combat, negates all damage against your fleet for 10 seconds
I have no idea if any of that fits at all, but general idea is one I find pretty exciting. Maybe it's totally unnecessary, I guess we'll see in testing.