Not bad, the first song that came on was nice, it seemed different from the regular Pokemon battle theme, had a very retro Final Fantasy feel to it, but also noticed not all the songs were Pokemon, you should probably keep it all Pokemon, or at least instrumental.
Improving the animations of the moving Pokemon would help too, as well as adding sound effects to the shooty things, and sound effects to the Pokemon taking damage (different sound effects depending on the type, and if it's super effective or not would be rad).
Interface could use improvement most of all I think. Everything seems a bit sloppy, and cluttered at the start, perhaps you should try and imitate the interface of the Pokemon games? With the pixel design, or drawn version, your current boxes with bevels/gradient shades makes the game look really, Flash-y. And, in my opinion kind of amateurish. Looks are important!
Keep up the good work :)