The Johto plot will technically start in Goldenrod City, but Goldenrod won't actually be important for a while, and in any case that map will need some modifications from the original. (There's going to be a jail added, for example.) So, Azalea Town, because it will be the closest to the same layout as in GSC.
After the disband, the main character will probably be stranded in Johto a while, so they won't be able to get to Kanto. When/if they're able to get back, though, I'm not sure yet. In G/S/C many Kanto routes were shortened, but since that was just to make them go by faster and not because of anything relating to the plot, I'll probably leave those routes the same as the originals. The biggest problems are going to be in Saffron, Lavender, Cinnabar, Seafoam, and the power plant, since those will have new maps... I'll figure out something. If nothing else, I can expand the size of the rom, duplicate all the Kanto maps, actually make a second Kanto, and then go in and change those few locations. And if that doesn't work, maybe the player will just never have an opportunity to go back to Kanto.