The plot was okay. It started out as a cookie-cutter "steal this Pokemon" plot but things got much more interesting in the second half with the whole underwater temple business, so it was overall fine.
There were several other positive aspects as well.
There was a lot of funny bits, such as the foreshadowing of Pokemon Diamond and Pearl, and Phantom's "there are two kinds of people" running gag. The fight scenes were, as usual for the series, very well-done, and there was a nice amount of very well-done emotional and cute moments surrounding May and Manaphy.
But the best part about the movie was the animation and direction. The obvious CGI got annoying after a while, but when it was 2D, it was top-notch. There were so many great scenes here. The absolute highlight was the FANTASTIC scenes with them going through the ocean. The music, animation, and atmosphere mixed perfectly to create some of my favorite scenes in the series. Other highlights included May's dream sequence, and the ending, which while not up to the climaxes of other Pokemon movies was still nicely intense. Ash going Super Saiyan was pretty stupid though...
Overall, another good movie, one any fan should enjoy.
