i think that they should have mixed it up like FR/LG and R/S/E had a lot of similarities like 5 same type gyms and every gen has a forest early on (viridian, ilex, petalburg, and eterna) plus they had WAY too many water routes
Add more water routes (I love water.)
I also would like to add a more climatic area. Cave of Origin was lacking when it came to how climatic it was, so I would replace it with something better(i.e: A huge mountain similar to Mt.Coronet.)
I don't necessarily mind the water routes, but they could make them easier to traverse, I know the first time I was going through the game I spend hours trying to find out where the hell Sootopolis was. I still had trouble my second playthrough.
Also, they could have done so much more with Aqua/Magma, instead of both of them going after a volcano Magma should have been after a volcano and Aqua could ahve tried to make a tsunami or something.
Also, blowing up a volcano, pretty evil right? NO THEY WANT TO HELP THE WORLD. Pathetic, just pathetic.
When I think about it, I wish their was Team Magma, Aqua, and the police force. I could see the sherrif telling you not to chase them, but you do anyway. It be nice to seed them catch a grunt and question him.