I actually liked the WC movie. What bothered me most about it were the stupid physics mistakes, such as gravity in space and the whole quiet thing. BTW, Sphynx, in the movie the Rapiers aren't jump-capable, when Blair jumped he went through some sort of gravity worm-hole distortion thingy.
And Ace, I'm going to have to disagree with your "better" storyline. That storyline would work only if people had some familiarity with the Wing Commander storyline - which most don't (I don't, I've only played WC4 and that was years ago).
I think the storyline they used was alright, just could've been done a whole lot better (minus the whole Pilgrim bull**** thing as well). If they had made it tighter, with less extraneous BS, and focused a lot more on creating likeable, believable characters rather than cookie-cutter "badass female lead," "hot shot pilot" "outcast hero" and "racist XO" then they might've had something that would've been recieved better.
And for the record, I also liked the ship designs in the movie. The Kilrathi fighters were rather uninspired (although we never really saw them), but the Rapiers were quite interesting (albeit a little cartoony). Again, with some minor adjustments we could have had a classic.