I think void pretty well organized everything out well.
Only thing I'm still iffy on is the legendaries. That is easily one of the hardest things to make work. I mean being able to use them WOULD be cool, but then the problem comes down to if they make them as powerful as a legendary is supposed to be, and well that would just take the fun out of the game. That's what kind of killed end-game for older pokemon games for me, the legendaries were tougher then anything I had to start, and just got tougher as they leveled.
I kind of think more along the lines of how SE handled FFXI and summons such as Bahamut. Their storyline related, but summoners can't summon them as they would have to reduce the power of Bahamut significantly and thus would kill his role of being so powerful story-wise. So instead they made him story only and a boss fight rather then tarnish his name by being summoned by every summoner and no where near holding the title of King of the Dragons.
Though I'm iffy on that whole subject cause I never cared much for the legendaries and how they replaced my entire party.
And sweet jeebus yes! I've been wanting that forever in the series. I hate how un-diverse the population of areas are in the game. Let alone the different types "Oh joy it's ANOTHER flying/normal/bug type....oh how wonderful. Get in line.".1. ALL Pokemon able to be captured in the wild. This means legendaries, starters, what have you.