Wow, this is looking awesome so far. Lovin the fakemon; it's not often you find a game with decently sprited fakemon n___n i know a lot of people are against fakemons but personally i like that it adds that extra touch of originality to the game. And you're are sprited so damn well.
I also agree with cruciFiction. Your comments were constructive at first, if a bit snippy, but stop dragging out an unnecessary topic Peeky Chew. Your comments have all been addressed, leave it at that.
As for the plot, I like that you've moved away from the traditional "evil organisation" and given the plot a more racial twist. Wars over beliefs and religion are real world topics and its nice to see them in games. I'm curious about the hero though; are you going to make both genders available and then simply have the counterpart be the crush or can a player only be female? I'm certainly not going to tell you how to co-ordinate your plot but having only one gender option might alienate a few players. I do like that you're adding some actual canon romance though lol, not something you see in the real games XD