I don't like the idea as much as anyone, but you know the retcon is going to happen sooner or later. They will have to change the story of the originals to compensate for Megas. (in fact, I'd like to see them somehow make a reference to the pink floral pattern pokemon line and have Munna somewhere around there) As for seeing Kanto at a later time, there is only one question that is brought to mind: who will be the villains? TR has been disbanded. Twice. There is no indication of anything at all. What, is there some kind of mysterious new boss? With his own quirky miniboss squad?
I actually kinda like the idea of merged Celadon and Saffron, that would easily create the giant megacity like Lumiose, and have features similar to it. Saffron's gym would obviously remain, and Celadon's has been changed to a greenhouse or something, complete with soil to plant Berries.
A new gym has instead been made in Lavender Town, in the Radio Tower. Here, a reality show-esque production is played out, where you face a mandatory string of battles before the leader themselves steps forward. The type? Fairy? (couldn't think of anything else that would fit) Also, there may still be things afoot in the upper floors...
Another gym that has changed is Viridian, though I am unsure what to do with it. I like the idea that Blue has moved on, but what in it's place? There are 3 types that could still fit there: Grass (since Celadon's isn't there anymore), Ground (this was it's original status under Giovanni), or Dark (it doesn't have a gym yet). Why only 3, you might ask. I am maintaining the matter that Johto and Kanto are one system, and thus their gyms still have to not repeat each other. I see no reason for Johto to have changed in that time, unless Pryce is no longer with us, in which case, that makes 4 now. In light of that, it might be a better idea to reopen the ninja hideout and have the Dark gym there.