I'm sorry but I agree with Warp Shadow. This has been attempted hundreds of times before, and it won't work.
To handle player control of a capital ship originally designed for AI to pilot would entail taking the FS2 engine and using it for something other than flight simulation. It would require very dedicated coders bent on making it happen without workarounds such as docked ship-wing-turrets.
Capital ship pilots cannot expect to just hop in and expect to use normal FS2 controls, or be presented with the normal fighter craft HUD. Hopping in a capital craft would turn the game into a naval combat simulator.
For one example, we can use Star Trek: Bridge Commander, where the keyboard controls movement and the mouse aims the guns and rotates the camera, as well as lets the player click on HUD controls. Very easy to learn, and does not overwhelm the player with too many options. In that game, you also get the option to delegate the AI (your crew) to control various aspects of the ship as needed (such as weapons and ship movement) so that you don't have to. Your only weapons are pretty much phasers and photon torpedoes, and the most you have to worry about is usually another ship or two. Some mods let you lock in multiple targets so that your phasers target multiple ships at a time, but this makes it more difficult to avoid completely depleting a phaser bank (usually, to keep phasers charged, the ship must be rotated so that different phaser banks are used to attack the enemy ship).
But FS2 is even more complex. It will have bomber wings launching Stilettos (or equivalents) at you while an enemy capital ship is braining the heck out of you with a massive beam cannon. You will be needing to be aware of the bombs launched at you, request your fighter wings to protect you from them, and manage priority levels of targets to help ALL your weapon systems (anti capship beams, anti fighter beams, flak guns, plasma cannons, laser cannons, missile launchers) prioritize what is most dangerous to your ship or your mission. You'll need to have the situational awareness (from your HUD and sensors) and the controls (from modifications of the engine) to be able to do everything that an AI capital ship in FS2 can do.
Some of it could be automated, some of it not. We'd have to decide on these things. For example, weapons might be handled by a targeting priority list, to decide where more of your weapons will fire at. This would be vital else you wind up unable to defend yourself against fighters because all your turrets are distracted by a capital ship.
You have to ask yourself, what would players be forced to keep track of? Would they remain as they are, merely piloting the ship in a sort of external padlock view while their weapons do everything else? Would they be able to take direct control over their weapons systems, even program in firing solutions? Can they group their weapons and fire them in unison? What about launching fighters? If the fighter bay is damaged, can fighters be launched? Will it break the mission if that happens? Too many options will confuse the player; too few will make flying a capital ship boring and uninteresting.
It's probably not impossible to get FS2 to have capital ship combat. The real question is if the FS2 engine is extensible enough to support adding a whole different "game" unto itself, and if the community really wants this that badly.
