I loved the integration of the Weapon X storyline, and the after-credits sequence actually makes me look forward to Wolverine 3. I liked the meta wink about how bad X3 was and that they seem to have taken it and the first Wolverine movie out of continuity, especially as that means they can do the Dark Phoenix with the Shi'ar in the next one if they choose.
I did have a few small problems with it apart from the aforementioned lack of characterization. For one, unless it's a bank account fight, an iq test, or a having sex with underage girls contest, Angel isn't going to beat Blob at anything. I hated what they did with poor Caliban, and making Psylocke a pure villain doesn't make sense to me either. Making Scott the ringleader of teenage monkeyshines doesn't seem right, though there was the suggestion that Alex's death would lead to the overwrought seriousness and sense of responsibility we're used to from him. That could actually end up being a decent bit of character building. The psychic plane fight was just all kinds of terrible, especially as the shape-changing stuff was in slow motion. It looked much better in the trailer.
But really I think giving a coherent explanation for Apocalypse's powers, age, and absence for thousands of years covers a lot of minor sins in my book, especially given the trainwrecks pretty much every writer has made of him in the comics over the years.