i'm thinking that the Flagship should be AI controlled (it has a set path to fly) so that some moron doesn't break the spawning area for mainline attacks
as for frigates and corvettes, yeah, i could see Players piloting those,
people could choose to spawn in either that flag ship (more fighter options, and heavy firepower) or they could choose to spawn in the frigate (you can fly close to the enemy, and you have some guns and cannons to help)
In Multiplayer matches, yes. But leave an option for custom games of player control, i say this because with knowledgeable flagship captains we cld see some very competitive game play.
I would also like to see a ships destruction affect it in more dynamic ways, for example. If a ships engines and or control thrusters are damaged or destroyed it will affect the ships movement capability.
I also love love the idea of having the frigates as a secondary spawn area. Its very dynamic because if you lose your firgates you also loose a spawn option. This would likely prompt players to think differently about how aggressive or rather non aggressive they want to be with there frigates.