Sounds sweet, you shouldn't make it like how the harpoons lock on. Just make it as simple as stilleto targetting. Target any part of the ship and when you shoot it goes there. The deimos flyable mission i tried a while was like that, just target the ship, turn your beams and pulverize. But the thing with the deimos was that it has slashing beams. So that means targetting on the colossus would need to be more specific, like subsystem and turret specific. Otherwise targetting a capship with a beam from the colossus wouldn't work. If you target a ship without anything specific like a subsystem or turret, where the hell is the non slashing beam supposed to know where you want to shoot the vessel. Nonslashing beams on the deimos flyable mission would make it even more powerful as the weapon would be a lot more specified than swiping a beam across a vessels hull.
On the dockable fighters thing, i would just imagine that it'd be like flying around with destroyables. You fly around with a lot more lasers and secondaries, but if one of the fighters in the chain gets destroyed(hopefully not a1), then you just continue to fly around with one less docked fighter. Or for balance sake, make it so that if one of the docked ships gets destroyed, it breaks the docking chain making your have to redock again.
Another thing that would be cool like bizzybody mentioning, is weaponry quadrants. Such as front, rear, bottom, left, right, and top weaponry on the colossus. Make an overwhelming colossus mission where ships appear all around the colossus, and the player has to switch between a bunch of the weapon quadrants of the colossus. Got a ship on your front...kill it, ships warps in on your rear, switch to rear view and weapons and kill that sucker on your ass...and so on. That'd be fun, and would truly make flying capships a unique experience since capships need to actually do that ****.