Even back as far as the early 80's when I started playing SFB...I flew Klingon. In fact, I have never flown as a Fred in SFB. When I wasn't flying Klingon in SFB, I was flying Hydran. I guess I have always hated that the "good guys" always win in the movies...much the same way as I have a general dislike for "pop culture." If it's popular on TV or the radio...I pretty much hate it. I'm a contrarian in some respects, I guess. I started flying Klingon from the start and I haven't looked back since.
Even when SFC1 came out, the first single player campaign I played was the Klingon one and the last one I played was Fred. On MPlayer, I always flew Klingon or Hydran. When SFC2 came out, I bought it, but didn't really play it until the D2 went public and then I was there on Day 1...as a Klingon. I think during that first week, I logged into on of the IPlay servers as a Fred and flew a BCJ for a little while. That got old real quick because those servers were overrun with Smurfs...heheh. I didn't fly Fred again until IDSL, I think...there were no Freds online (which was weird) so Bonez and I decided we'd go be the Fred navy for a while. Once the usual Smurfs started showing up, I swtiched back...though I did really learn to enjoy the F-DDG and I felt like photons hit just fine when you used them right...heheh. That doesn't mean you'll ever katch me in a K-D7T, though!
Most of my SFC2 time has been spent flying Klingon, of course. I've flown a good deal of Romulan, ISC and Hydran, though, and pretty much enjoy them in that order, after Klingon.
I have never felt comfortable flying Lyran, oddly enough...I feel like they out-Klingon the Klingons, but I just can't get used to them. Maybe I just need to make more of an effort. I enjoy flying Gorn, too, though I haven't done that much. For plasma, I prefer the Romulans because they can actually turn and I'm fairly used to having the inferior phaser suites...heheh. As much as I enjoy my Kzin friends, I simply hate their interface....drives me crazy, so it's hard for me to get up the gumption to fly them much anymore, though I have spent a fair amount of time in the past flying Kzin.
I think as far as the Freds go...I don't like the interface much and I think I'd rather fight them than fly them, anyway. There's nothing wrong with their ships, though and a lot of good guys can be found in their ranks.
So...I guess I basically chose Klingon in SFC2 because that had been my history with SFC1 and SFB. In the "real world" I like the good guy to win, but when it comes to the world of entertainment, it grates on me that the "good guy" always wins...there's always some deus ex machina that saves the day and it bugs the hell out of me. Sometimes, that "good guy" mentality has gotten displayed here in this community and it has bugged me, too. Maybe it's irrational, in a way, but I don't like the idea of SFC being about "good guys" and "bad guys." I don't think any race in this game has any claim on the title "good guys." As a Klingon player, I don't view myself or my comrades as "bad guys" at all. Say what you want, but it isn't easy always trying to fight through the "history" Paramount and ADB have written for us.
I also have a propensity for backing underdogs and in this respect, I see the Klingons and Coalition as the underdogs. SFB history and tech wasn't written in their favor and thus, neither were the games in the SFC series. I guess that's probably why the Klingon Empire and the Coalition in general always feels like home. It works out well that I find that with very few exceptions, the Klingon playerbase consists of some of the nicest, most honorable people you'll ever meet and they are just nails to wing with. I think the overall mentality/attitude of the Klingon regulars has changed a bit from what I remember it being "back in the day" when SFC2/D2 was at the height of its popularity, but these are still good people worthy of spending time with. I have friends among the other races and have enjoyed my time with them, but I always have the most fun flying Klingon/Coalition.