This is a really fun idea, but I definitely see a huge advantage for Kanto teams, not only in number of choices but also the relative strength of those options. If you'll have a look at the OU Viability Thread, specifically look at the S and A Rank pokemon. You'll notice they're almost all Kanto pokemon, and those are really the main pokemon used in OU.
Without totally throwing everything out the window, the one thing that could really help balance this out would be to just add Hoenn to the mix of valid Johto pokemon. The balance would still probably be tipped in Kanto's favor, but not by such an extreme.
