Let's see:
Bad jokes.
Completely bastardizing on of the most well developed and simple to pull off vilains in Marvel.
The team never actually did anything even remotely Fantastic Four like.
Instead of having actual character developement, they had a five minute comedy montage in the middle.
The best thing about that movie was Willie Lumpkins. Of course, since Lumpkins is such a stone cold badass, that ain't hard.
The tone for the FF film was completely tung in cheek crap. The tone for The Avengers should actually be
good. Way I see it, it should be like a James Cameron flick. Crap loads of action, some deep parts, and even a good bit of humor thrown in now and then. But not the camp fest that was Fantastic Four.