Well Dogasu has covered the synopsis pretty well there so there's not much I can add to that. Here's a small review/impressions to follow it up.
From the start I want to say that overall I'm impressed with the movie. It was an enjoyable adventure for the most part.
The "this is the world of pokemon" spiel at the start of the film was, as Dogasu said, a little long and seemed to be kinda fillerish and pointless to be frank.
Right from the word go the movie itself was showing promise as it attempted to take a more mature take on the battle between Deoxys and Rayquaza. Looking at it through the eyes of the audience majority (6-10 years old) it would have been quite a scary experience. There was excellent use of camera angles in the battle and edge of your seat stuff as young Toh'i is caught in the stampede of Sealeo and Walrein.
With the prologue over the movie slows down a little again but builds up to the battle tower quickly enough so we're not getting bored. Team Rocket's entry was less than spectacular, it was very similar to the 2nd movie where they run headlong into a rock, but in a much more boring style. The battle tower battle was a little one-sided but was fairly entertaining as Ash's Pikachu and Torkoal stumbled over each other.
After this they introduced the side story of Ash wanting to help Toh'i overcome his fear of pokemon. This made the movie feel more like an extended episode from the series at times. The scene with the pokemon playing happily together is pretty much an obligatory scene with these movies but it is probably better suited for the pre-movie Pikachu short film rather than in the middle of a movie where the audience is waiting for things to happen.
Enter Deoxys and his shadows which start kidnapping people and flying off with them. It's quite a cool scene with Pikachu and Ryuu's Blaziken firing attack after attack destroying the shadows in an effort to hold them back.
The windmill scene with everyone helping to restore power... well yeah for the story to work it's necessary but it seems to play out like a moral about teamwork than anything else and you're left kinda shrugging you shoulders and thinking "eh".
Rayquaza gets inside and the battle between him and Deoxys resumes and it's played out very well except for the limited attacks used by both pokemon. With the entry of the second Deoxys they could have ended the movie but I think it worked better that they kept going because Rayquaza was still kinda pissed off and so it's two Deoxys vs Rayquaza and the Deoxys don't seem particularly interested in fighting anymore.
The scene with the robots going into attack mode was pretty unneccessary I think. It extended the movie more than was really necessary and didn't really achieve too much.
But as I said at the start the movie was very entertaining even if the plot lagged at times.
Now technical points:
As with the previous movies there was a lot of CG animation used and it looked very nice actually; however there are points in the 2D animation where you wonder if they ran out of money because of the CG as it gets really sloppy sometimes which is disappointing.
The soundtrack was for the most part very good but I swear if I *ever* hear that L-O-V-E-L-Y song again I will go on a murderous rampage. The song was *way* to repetitive and the tone and pitch was not nice on the ears.
As I mentioned eariler the camera angles during the battles were very good and that is the same for the whole movie. There was some great use of a variety of shots and angles that kept the interest up.
To finish up I've gotta mention that the star of the movie (at least in the kid's viewpoint) was Gonbe. Everytime the little guy appeared the kids were very excited about it. And he was very cute in his role to be fair.
Right. I've rambled enough I think.
Another solid movie overall.
Oh and one final point that Dogasu didn't mention. At the very end of the credits all of the pokemon who had appeared in the movie aside from Deoxys and Rayquaza were dancing the aforementioned song with pom-poms; even Blaziken, Blastoise and Metagross. We all felt very sad for them.