I think we can all agree that the distribution of Pokemon across Johto and Kanto needs to be reorganized (if only one thing is changed, please let it be this one!). While it might make some kinds of sense to have some species of pokemon available only in Kanto (and having the same true of Johto- Jynx, for example), the decrease in enjoyment of the game it brings isn't worth it. Let's be frank: Houndour and Murkrow are freaking cool pokemon. What fun is it to catch them at level 14 after beating the Elite Four?
Another issue I took with the G/S/C population map was that it seemed like they went out of their way to make dark and steel type pokemon harder to find (with the exception of Magnemite). IIRC, in addition to only being available in Kanto, Murkrow and Houndour were pretty rare, steelix and Scizor were only available through trade, and Pineco was one of those you had to headbutt trees to find. I could be wrong about Pineco though, it's been years since I've played those games.
I hate to sound like a broken record, but frankly toss me in with the "up the gym leader's/E4 power level" crowd. A level 50 dragonite simply should not be the pinnacle of Johto pokemon, even if there's another half of the story left.
And finally, on a more speculative note, I'm interested in seeing how they manage to bring things up to snuff with D/P/Pt in regards to evolutions and wireless activity. They'll have to fit both the GTS and the Battle Tower in somewhere. Same with the underground. And what about Magnezone and Probopass (let alone Leaf/Glaceon)? How will they fit that in? Will it be changed to Mt. Mortar/Silver/Moon? Or will they just not evolve? If they do fit in those evolutions somehow, will Leafeon evolve near, say, the Ilex Shrine? and Glaceon in some room in the Ice Path?
EDIT: broken sig. Figures.