First of all, this is a very fun and good looking game. The only thing that bothers me is some of the Fakemon sprites. It's not that the designs are bad, (most are quite good, actually.) it's just that some of them don't fit into the art style of the rest of the pokemon. In battle, they feel out of place. (Especially Furunny. I inwardly cringe every time I encounter one.)
For instance: Chirpich's regular sprite looks great, but its back sprite is awful...
I'm not asking you to get rid of them. Rather, I think they need to be altered or maybe even redrawn to fit more with the pokemon art style. I'm no sprite artist, so I'm afraid I don't have any concrete suggestions on this kind of thing. :(
Anyway, that's just a small peeve on an otherwise awesome game. Besides that and a few places where the ground looks awkward (sharply angular ledges in some areas) this is a fantastic game. Get someone to thoroughly go over the fakemon sprites, and you'd make a great looking game look even better!