I recently decided to play the original Halo again (now don't get me wrong, this has nothing to do with Halo), and I was playing the first level and saw the boarding ships, and got an idea.
What if Sins had a special structure/frigate/Capital ship that sent out boarding parties, which eventually took over the enemy ship/structure?
They would be as small as the fighters/bombers/ and would converge on an enemy ship.
This would also lead to a new part of the tech tree, having your ship's anti-boarding defences (turrets that destroy them, marines/servicemen stationed inside of ship for the sole purpose of dealing with them, etc)
Once a ship is taken over, it would be transferred to the command of the player who sent the boarding parties, but it would not be able to use any special skills the original owner had purchased.
But of course, boarding won't be real easy. Enemy fighters would be a huge threat, as boarding parties have no defences. And, even when boarded, it all depends on the ship/structures defensive levels, and the boarding party's offensive capabilities, and size of the party/number of ships that breached defences.
Just a thought, I'd be happy to read your opinions on it.