It seems that the Federation always ends up being the "bad guys" as it were <_< , and I always thought that there should be a different Fed. storyline where the player joins the Federation Navy, gets some new Fed. technology and the opportunity to get some upgraded ships or perhaps have a specially upgraded Carrier forced on the player (not unlike the Unrelenting).
P.S - I'd really like to see this plugin happen but I need an experinced programmer to set mission bits, have systems change governments and the like.