I appreciate the idea of the command system as a way to organize the endgame content. But I think it wouldn't be hard to make some lore background to all of it, creating some kind of minigame, like a galaxy map interface where you can manage your Alliance.
This way, maybe what you do in endgame stuff (heroics, uprisings, flashpoints, ops, pvp, etc) could affect your map, and you could help your Alliance to conquer and keep planets and maintain your power base.