I've never had a problem with X2 remaining the best of the franchise.
To be perfectly honest, walking out of X2, I always felt that no X-Men 3 would surpass it.
I admit, I got caught up in the hype, when the 2nd trailer was released. I felt that from what the trailer showed, the movie would have the same drama and emotion of X2, but the action was going to be through the roof.
However, seeing some clips (Jackman's Leno clip, Janssen's Kimmel clip, and the 7 minute clip), as much as I enjoyed them, my hopes went down a little bit. I realized that the movie WASN'T going to be on the same level in terms of drama, and therefore, wouldn't be as good a film.
In my opinion, action is only good when there's good drama to back it up. I like action films with depth.
Now I still think this film will have a good sense of emotion, just not the way that Bryan Singer did it. And this film will be through the roof in terms of action, and fan goodies.
Overall, I think in the end, X2 will be the superior movie. That will be the best installment of the trilogy for all time. But I think that X-Men 3 will offer something that X2 didn't, with it's balls to the wall action. So in a way, they will both be about equal, because they will both deliver something that the other didn't.
I will think that X2 is the superior film in terms of smart filmmaking, however, and therefore, remain the better of the franchise.
But I don't think that's a bad thing.