Kyle is right (Oh god, here I go again after said it about million times on the PB forums) there's no evidence of Kanto being included, you'll probably only go through Tohjo Falls, route 23 and 26 Victory Road and route to Mt. Silver in Kanto. The right gate in the Reception Gate before the Victory Road might be closed. They could just lock the exit to Viridian City, so you only have access to a small part of Kanto. (just like in GSC before defeating the League)

The only use where Kanto was for was defeating Team Rocket and beating some gyms. Beating gyms is ''useless'' doesn't affect the story much. And since they've changed already a lot to the story (Kimono Girls everywhere around, Eusine walking through Johto, new areas) It wouldn't hurt then to make the last battle against Team Rocket appear in Johto too.