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Johto technically never had a 3D game either. And technically it's also next in line for a remake because HGSS came before BW, so Johto is currently the most out of date region.
I think that there won't be any Gyms at all this time around. Instead I expect there to be rival schools that you travel to compete in tournaments and win them for your school.
It's already been confirmed that this is not a reboot. A preview showed off a whole bunch of Ash's trophies, badges, and keepsakes from previous sagas.
They might, although I think that Gou would be a bad replacement. A show about mindlessly catching Pokemon would not be a fun show to watch, in my opinion.