I think this project looks really nice. I've been following your progress for a while now on dA and am happy you've finally made a thread! I think everything is very well done and organized and they seem to all fit together well. It's not sloppy!
The only problem I really see is the starters. They just don't seem to be match up well. Tyrogue has a split evolution, where it could quickly become an unfair advantage to pick that, while Poochyena and Chingling have one evolution per. I'd consider choosing a different pokemon for the fighting starter.
Maybe Makuhita or Mankey? They're both pure fighting types and are two stagers.