These ideas are really fantastic dude, I love all of the stuff you have here, I'm glad to see people here aspiring for big things rather than just compromising. I really look forward to seeing this game become a reality. Also I suggest trying to acquire RMXP [lets just say doing so for free isn't so hard]. Also, is the wiki down? I can't seem to access it.
One suggestion though is to add more filler towns, you have the starter town, then 2 gym towns in a row. No Pokemon game really does this since they want there to be a disparity of levels between gyms and they need to give the player time to level up to meet the second gym's levels.