I have to say you've done very well with this. Those interactive battles are a very interesting concept, and thankfully they work near perfectly. Normally I hate sprite flashes nowadays but this one is something... dare I say, different?
Voice acting was for the most part exceptionally good, although a couple of your actors sounded like they were talking a little quietly (Professor Fennel for example). Everyone else was fine, especially Seymour who did a stellar job as Gallade. The use of 3D was a nice touch, and the file size didn't suffer terribly much for it luckily.
If you continue to implement interactive battles (and you should as there is good potential here), all I would suggest is you clean up those attack effects and make them a little prettier. I look forward to the next installment. :>