I have considered using a mass-import to fight Red, but I realized how redundant it would be to have four seperate rebellion plot-lines, so I changed a few plotlines around. Part Two is in Johto, will be Crystal, and I am still debating two plotlines. One of them is a rebellion, but it is completly different than what one would expect. The other plotline involves more of a non-connected prequel, with explanations about the Mewtwo incedent, the empire in Johto, Lance, Bill, Oak, and the foundings of Team Rocket. I haven't decided yet, but I am strongly leaning towards idea two. I am trying to get Vappy and Ivy into the sixties, with Aero, Media, Icy, and whatever I catch in Victory Roar in the fifties. Otherwise, I can see Exeggutor, Alakazam, and Gyarados being very painful.
EDIT: You do realize that Red is the protagonist of Part One, right?