A political story, involving the president of the UFP and possibly a coup/collapse/assasination to get the story going.
Bureaucracy, wars and overextension of Federation borders leads to disatisfaction with members of the Federation, some consider leaving in the wake of heavy Borg and Dominion aggression and the incurred deaths of their people in these conflicts.
Picard is promoted to Admiral at last (or maybe just retires as captain), with the handing over of the Enterprise (E or F?) to a new captain (Riker or even Worf or maybe someone new). Starfleet appoints Picard to take over as temporary UFP president after the assasination and the story involves restoring order to the Federation. With lack of control/federation enforcement, factionalisation takes hold, permitting the Dominion/Cardassians to begin rebuilding a threatening fleet. While supressing these breakouts, a major threat to the Federation is revealed from within
I'd like to include the race seen in the season 1 TNG episode 'Conspiracy'
http://www.jammersreviews.com/tng-1/...php#conspiracy
Which involved malevolent symbiote creatures infiltrating Starfleets highest positions. The episode was set up for a sequel as the review (see link above) points out, but there never was one. Maybe a whole fleet for this race could be invented for the game?
I'd love to see an Armada 3, I was kind of disappointed when I saw what Legacy turned out to be (Bridge Commander with better graphics but less control and gameplay)