Maybe they can elaborate more on the whole Magnet Train dilemma. Last time, it seemed like they were going to do something more with it, but they couldn't because lack of memory space. That's probably why there was only one Rocket grunt in Kanto. Due to the power plant missing a machine part, some towns in Kanto could have a power outage, meaning you can't access certain gyms. Once you fix the Magnet train problem, you can go to the other gyms. Those gyms you were unable to access earlier will have higher levels. Creating more of a challenge in the game.
Other things they can do:
~Open the Safari zone and make Hoenn and Sinnoh Pokemon available there after the National Dex is obtained.
~Open Cerulean Cave so you can battle powerful Pokemon so your Pokemon are strong enough to battle Red.
~Make the Seafoam Islands have a building and have some trees. The building can be Blaine's new gym. (That is, if they kept the idea of a volcano erupting in Cinnabar.)
~As for the place where Cal is, maybe they can add more trainers.
~Maybe they can have a contest building in Kanto (Vermilion City to be exact, seeing as Machop has been stomping the land flat so they could add a building there.) In the contest building, you can compete against: Leaf, Red's Mom, Jasmine, and Will. (I chose Will of the Elite Four because he seems to be the artistic type who would do very well.)
I don't know if anyone mentioned these before. If anyone has, please forgive me.
~Ashley