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>Region
Sinjoh. Yeah, that's right, we're going there. You start out in Sinjoh, and you get to go out on your adventure. Sinjoh consists of three small towns, and a lot of ruins. Mostly unexplored locations, and the first Gym is in Sinjoh. But here's the kicker. You get to choose; North to Sinnoh, South to Johto.
If you go south, you'll come down through Ice Path into Blackthorn City. Now the Region will only have 3 Gyms that are challengeable, but there will be loads of quests to do, and you'll get to see how the Region has changed (This is a Sequel to HG/SS/Pt.)
After defeating the three Johto Gyms and obtaining Fly, you may go back to Sinjoh and head North to Sinnoh.
YOU DONT HAVE TO DO IT IN THIS ORDER.
If you choose to go to Sinnoh first, the three Gym Leaders there will have lower level Pokemon, obviously.
The final Gym Leader would be on the Island North East of the main Sinnoh Island. Surrounding that island are 4 others. Each one has a Member of the E4 on, and you get taken on a boat tour for your E4 experience.
Pic Related, Shitty Drawing you can use to follow my poor description of a potentially awesome Idea. Oh, and Kanto is the post game.
>inb4 "That doesn't look like Japan, it's too small"
It's already been established that Regions are inspired by real locations, but dont fit the same way in the Pokemon world. They could connect Kalos and Unova in Z for all they cared.