Some people here made a very good reasoning about how it's possible that the versions of how Blair and Maniac got on the Tiger's Claw together could work in all three variants at the same time, but I simply know that such a thing was never conceived of. Face it... when you're playing WC1, you're INTRODUCED to Maniac. In the movie, Blair and Maniac have never SEEN the Tiger's Claw, and in the academy series, they're stationed aboard the Tiger's Claw in a modern version of Midshipman's tour. Face it, the puzzle doesn't fit together, it was never MEANT to fit together, and there's no sense trying to shave the pieces to MAKE them fit together.
Point of order, though, Wing Commander Academy isn't about their time at the academy -- it's a command school of sorts, and all the episodes on the Tiger's Claw (2-13) take place *after* the movie. The idea is that they're competing for command of a wing of cadets, which is what the medal ceremony at the end of Glory of Sivar is all about.
I did a timeline skeleton that breaks down everything fairly well:
https://www.wcnews.com/loaf/skeleton.htm (I believe it's wrong about one WCA episode, though -- "The Last One Left" should go in early April '54.)
I'm not pretending to be privy to the inner workings of EA or Paramount, but I do know that as you peel off the onion what you come down to is that they make a product to make money - a product makes money if people buy tickets and CD's and action figures. Star Trek has a fan base umpteen times bigger than Wing Commander but the latest incarnation didn't make it because there really wasn't a whole lot of care put into making it. Very much like the WC movie, which is what comes to mind to most non-gamers when you mention Wing Commander. I really hope that Wing Commander comes back to life, would I be at the CIC if I didn't? But if it's going to, it's going to have to go back to its roots.
Except you're in a tiny "angry internet" box -- the fact that SUPAKILLA42069 hates the fact that Enterprise doesn't have big space battles isn't why corporate decisions are made (heck, look at the current season -- SUPAKILLA42069 will tell you that all the blatant fanboyism is Season 4 scripts is amazingly great... show's still dead). The tiny minority of people who care about continuity error A in main bus B *do not matter*.
And again, I would argue that Wing Commander is not recognized as a bad movie -- it's simply not recognized at all... the movie wasn't universally loathed, it just wasn't seen at all.
It is very, very hard to prove a connection between Wing Commander "dying" and the commercial failure of the movie. The Prophecy team was laid off *before* the movie came out... and Privateer Online was brought back and developed *after* the movie came out. The movie cost EA nothing. All they suffered was a lack of publicity...
(I won't pretend to know about the inner workings of Paramount in the way I do EA, but I am fairly sure that a lot of the problems with Star Trek *financially* have to do with some pretty restrictive marketing practices on Paramounts practice in recent years than it does whether or not Klingons have ridges. After the big resurgence in interest in the early-mid 90s, Paramount decided they wanted to have their cake and everyone elses when it came to Star Trek... and things like action figures/comics/sourcebooks/etc. became more and more expensive to license. That eventually lead to companies deciding they couldn't profit by doing action figures/comics/whatevers, and it became more and more a niche market... and with it went a lot of interest from average fans.)
Also, re: fan projects. PLAY STANDOFF! It is stylistic, it's respectful, it's well written and it's fun. Privateer Remake is great for bringing awareness about Privateer -- but most of us already play the original.