I think people here are getting mixed up as to what the OP meant by 'flagship'. It is possible I am mistaken, but I see some posts that seem to think he's talking about Titans, others that seem to think it's the 'Fleet leader', and then a few that seem to have it right. To clarify, there is a 'last flagship standing' win condition in Rebellion, in which you start the game with a capital ship that must survive the whole game.
I like the flagship game mode... alot. Though I do think the game modes should have more options to them. For example, maybe losing the flagship doesnt lose you the game, but severely handicaps (ie you loose half your fleet supply , permanently, and can no longer upgrade your supply). In general, I'd like to see the game modes much more tweakable. Think of the multiplayer options for halo, and you get an idea of what I'm shooting for.
That being said, I could see flagships getting Auras that affect how you would want position them, but nothing drastic. Some possibities (obviously not suggesting all get implemented):
- 5% damage boost to nearby ships
- -5% income rate to nearby planet
- frigate capturing (long cooldown)
- +5% regen and healing rate to nearby ships
- +1 armor to nearby ships
- -10% turning rate to nearby enemy ships
On another note, I suggested a long time ago that I think "fleet leaders" (aka thing-formerly-known-as-flagships that are created when a fleet is formed) should give bonuses as well,