Quite simply, well done with this. The interactive battes are a very nice touch, and the voice acting is still very well performed, even though the cast was drastically cut since last time. Love how the story is progressing so far as well, it's a much darker take on the Pokemon series which is normally very corny and kiddy, yet it doesn't take itself too seriously. It really makes me want to crack out the Gameboy and play the games. I noticed the plug for Eastbeast's Shyguy Flash too. I've seen the beta and think you guys did very well with that too.
As for the negatives (don't worry, there ain't much) I still feel that some of the animated poses of the Pokemon during battles are a bit jumpy (Houndour for example). As for the line art you made during the credits, could I suggest you stay clear of gradients? Sometimes you can get away with them with backgrounds etc, but I just feel for characters (especially anime style) they need to be shaded manually otherwise they look out of place. Takes a little more time, but the end result looks that much better.
All in all though that's all I could find wrong with this. Well done on Daily 4th, I'm just glad there are still some good sprite flashes left out there. Good stuff. :>