I loved the first two movies. Exciting, great effects, cool characters, terrific stories... then you come to that 'awkward third album'... And yes it is awkward. But not a disaster by any reckoning. The story is good, the effects better than ever, the characters dynamic. So what's the problem? They simply try to squeeze too much in. There are loads of new characters, all demanding their air time, with the result that there simply isn't enough time for everyone to get a decent crack at things. It would've been far better so cut some of the minor characters to give the leads more time. Plus, some of the editing decisions are VERY questionable. For example, the battle at Jean Grey's house involving Wolverine and Storm... well, in the movie, it looks like they lose it to me. Not what you expect from your heroes. BUT... stick on the extra features and see the extended scene, however, and you get a very different picture. And a far, far superior scene. The finale has some similarly baffling editing.
So, when the action scenes are questionable, and the main characters don't get enough screen time, is it any wonder the movie didn't come up to expectations?
All this said, it's still a great movie. Not a triumph, but a worthy addition to the franchise.