I'm not sure if it's fair to compare Pixar to any animated film. Because of that, I made comparisons between Megamind and Despicable Me (Also came out last year) and found Megamind to be a much better movie.
I agree, comparing it to The Incredibles really isn't fair, but they are superficially similar in tone and are both super hero satires, so I just found myself unable to stop making that comparison. This may just be me and how my mind works.
Despicable Me on the other hand was lampooning James Bond style villainy, something Pixar has not done before, and so it avoids those kind of comparisons. I also thought it was a better movie than Megamind, mainly because it was more original. (How To Train Your Dragon and Toy Story 3 are much better than either)