maybe instead of how it happens in the games (where blue is the champion for an unknown amount of time before the player comes along) it's more of a race to the finish between alis and jacred? like they're both simultaneously fighting the elite four and racing to be the first one to reach the champion's podium, culminating in their final battle

alis is red-green colorblind

also i think there's plenty of times where alis and makoto travel together. so they experience some story events at the same time i think.

it's also important to remember that mewtwo is not truly tied to team rocket in the games. dr fuji just did that