I'm loving the game. It still have it's bugs but I can definitely see this game shining in a few months as everything gets polished.
That said, there was something I was thinking about while playing...
Except for patrol, defend, and exploration missions, everyone plays the same missions in the same order as everyone else. I would be great if there could be parallel quest chains and sub quest chains.
Starting after the tutorial mission, the player ends up on Starbase one where they could then be faced with two possible tracks to pursue... they can help with the war with the klingons, OR they can help with the Romulan situation. As players progress through those missions, there would be sub-arcs that last for 3 or 4 (or more) missions. This would be great, I think, because one player might be focusing on the klingon path of missions and his friend may ask for help on a mission that happens to be in the romulan path.
These two initial paths could, in theory, continue all the way through to Admiral levels, but, for instance, at Commander level, a new mission path begins revolving around the cardassians.
As it is right now, it feels simply like first we do then klingon missions THEN we do the romulan missions, THEN... etc, etc.