I think that the timing of the release of "Megamind" hurt it quite a bit. If you look at the revenue for this film, it really is not that impressive, as it cost nearly as much as it made. However, "Despicable Me", which came out shortly before "Megamind" made a ton of money--many times what it cost to make. Now this does not mean one film is necessarily better that the other. I really think that "Despicable Me" stole "Megamind"'s thunder and people were just not interested in seeing two films about an evil genius.
So what's my verdict? Well, frankly I think both films are about equally good but have a slightly different audience. "Despicable Me" is clearly marketed more to kids and has cuteness as its advantage. The minions from "Despicable Me" are magnificent and adorable. It's also a tad formulaic--but not bad at all despite the predictability. "Megamind", however, is more a film for teens and adults--as cuteness is not really something I'd associate with the movie. It also has a few more surprises and a more adult sense of humor. My wife and oldest daughter preferred "Megamind" while I preferred "Despicable Me"--but we all agreed that both were really nice films.
I could say a lot more about the film, but since it's now out on DVD and already has a ton of reviews, I'll pass. Suffice to say it's well worth seeing and is excellent entertainment.