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You know what I didn't like about Origins? That they KIND OF retconned gen VI into it, but not all the way.
I thought Mr. Fuji giving Red the mega-stones was great. I can see that happening.
Hell, even Charizard's evolution into Mega Charizard X was pretty damn awesome during the Mewtwo fight.
No, what bothered me was that Professor Oak mentions the Kalos region, and then towards the end, is talking with Red about how there are only 150 Pokemon.
If Professor Oak knew about the Kalos Region, there is absolutely no way he only thought that there were 150 Pokemon.
Either DON'T MENTION KALOS, or acknowledge the existence of the other 650 Pokemon.
No half-measures, Pokemon. You can't do that.