I wouldn't really think Team Rocket would end back up in Kanto. Their original plans failed at their first attempt and to see that they have moved on without Giovanni to a new region, I wouldn't see them returning. However, things can take a turn for the unexpected with Giovanni making an appearance for his lead role as Team Rocket Head. This is when I can see a new plot for Kanto, but I would place that is wishful thinking right now. With this being said, I would believe in order for Kanto to come back alive, different side quests and plots will need to have implementation to the game. As for the original male and female Administrators from FRLG, they are most certainly the ones to return. However, seeing as they were higher than grunts, I would find it easier for them to round up the past Rocket members to target elsewhere.
As for Jesse and James, I wouldn't rule them out so fast, because there is a chance for them to return. A lot of variations are being put into the game and I wouldn't be surprised by this if it were to happen. I would like it to though as a little anime interpretation would be nice, however it is true the game doesn't follow the anime. So, I doubt it as well, but you can always hope I guess.
As for their Pokémon, if the Pokédex follows the DPPt format where we need to see them all before obtaining the National Dex, then I can see a few modification in rosters for Team Rocket. It wouldn't be a bad change either as like I said, it may make them a bit more challenging for the game when including the raise in levels and movepools. However, if not then I can see the game taking its original course, but I would prefer a little alter. Not to mention, a slight alter in their team rosters would not have to be major. For example, with Team Galactic in Diamond and Pearl compared to the Galactic grunts in Platinum you will notice that they have changed their rosters slightly as well. So something like this I would think might be fine for the least.