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!
I was playing Call of Duty zombies with a friend once, and i had a brainwave.
Make it a 5 player ground stf with omega marks and fleet marks as a reward.
The idea is rather simple, the teams has to survive as much waves of borg as possible, for every wave survived, you get 10 fleet marks and 15 omega marks, every 10th round the reward doubles as the borg get more difficult and in greater numbers.
The premise is the longer the team survives, the more rewards the team gets, if you all go down, its game over.