Here's what I would do for the first game.
You can play as Red with his Poliwhirl, then recieve the Bulbasaur, than catch Pikachu, all in story events. Then you can do what ever you want, but RPG style, so its kind of like the original Pokemon games and Colosseum mixed. You go through all the gyms, LT. Surge, Sabrina, Koga are all bosses.
Through out the whole game you have to battle Green, your rival, and you meet Blue, the secondary rival who stole Squirtle, and she has her own sub-plot. Then once your team defeats final boss Zapmolcuno, you think its over. It's not.
You battle Giovanni, save Yellow from Dratini, then team up with Blaine to capture Mewtwo (SEPHIROTH!). If that wasn't enough, you have to beat Green after a string of battles at Indigo Plateau. Red becomes champion and then the credits roll.
I think it would be cool if after you beat the game, you could go back and play the game as like Blue, from when she steals Squirtle to Indigo Plateau, but the secondary game would be extremely short in comparison to the main game.
There would also be a demo for the second game, Yellow Cabarello. Even though there is zero percent chance of this happening, it would kick ass!