Remember that cool starbase in the mission Divide at Imperia. That was an awsome fight. A stf or other form of Q'd instance where you fight a starbase in phases would be awsome. It could be a phased battle in which the base alternates between using its hangar bays and torpedo bays/turrets. A starbase would make an exellent space boss. And, once your team has disabled the base it's time to beam down to finish off the captain!
How about a pvp match where both teams have a starbase to defend and the objective is to destroy the enemy starbase!