So why are we giving credit to the opinion of Sheldon Cooper's mortal enemy here....
As for what he thought was wrong with the film perhaps he should he should dissect his own body of work in The Next Generation.
Um... he already has
He's only done this extreme criticism of the character just so he remains relevant to fans, which I believe came around when he was dubbed the "Jar Jar Binks of Star Trek." Personally, I find the character of Neelix more baffling than Wesley Crusher, but you don't see Ethan Phillips or even Ahmed Best for that matter bad mouthing the way their characters were written or for the shows that they were paid to act in. Sure, the first season of The Next Generation isn't great, but at least you got paid to say your lines. Wheaton loved every minute of attention he got on the show, because he was a fan himself of the original show and it was a fantasy fulfilled to be a part of the crew of the Enterprise, just like Justin Long's character in Galaxy Quest. Wheaton should feel lucky to have been given the opportunity, because his part was originally written for a young woman and I seriously doubt that a real female Star Trek fan of his nature would have been chosen for the role.