I don't think that's entirely the case; certainly, the final cut of the movie has problems and some of them go back to the heavy cuts... like the lack of the intended climax onboard the concom. At the same time, it's not a case of simply bowing to public pressure -- the cuts were made by the director to fix things he thought were wrong with the film.
- The longer cut of the movie requires several extended scenes of the Kilrathi -- including ones where they're interacting directly with human actors (conversing with Wilson, fighting Blair). Chris Roberts wasn't pleased with how the Kilrathi looked and wanted to de-emphasize them throughout.
- Test audiences were likely exactly right about the traitor reveal; it lacks punch. You're shown a mysterious space-suited traitor several times... and the reveal is that he's the man who appeared for under a minute in the introduction? There was no reason to remember who he was in the first place, much less be shocked that he was betraying the Confederation.
- I'm sorry, I can't read the script without thinking Merlin is dumb and that we're lucky we lost him. He's Episode II C-3PO times a million--awful jokes that are completely out of tone with the rest of the movie. The film suffers a lot because the exposition he's supposed to provide disappeared suddenly... but boy am I happy I don't have to tell people I'm a fan of the Star Wars knock off with the tiny CGI wizard pal.
Restoring the cuts wont' change the issues people had with the movie, either -- it still has the same big World War II tropes, the same strange ships, the same rubber Kilrathi, the same Freddie Prinze Jr... it's an interesting thing to see, for sure, but it's not an ultimate fix that will make Wing Commander a guaranteed classic.