There would be no story... at least, strictly speaking. Not a cohesive one, anyway.
I think what a lot of people tend to forget is that in Gen II, plot barely exists. The only reason why traveling to Kanto and Johto was as seamless as it was is because they both shared the same villainous team that you had to run into every time: Team Rocket. Other than that, going to Kanto was essentially a repeat of Johto -- beat up Gym Leaders and fight the Elite Four and become the Champion.
If there were ever one game with multiple regions, it
can't have a cohesive story without spiraling into a hot mess. Unless all of these regions share the same evil team, same culture and everything else, I just can't see it working.
And if there's no story, there's no character development to go with the story. It'd just be a giant psuedo open-world Pokemon game where you do absolutely nothing but beat Gym Leaders left and right and fight multiple Elite Fours.
I appreciate your thoughts but i asked to ignore all the other problems it might face.