This thread deals with both Team Rocket's eventual return to the show, and Ash's destination after the Unova League. Since it pertains to two different (but connected) topics, I think that creating a new thread is warranted.
As we know, the recent two-parter ended with Team Rocket returning to Kanto. Some people interpreted that as being their farewell, but that impression is not supported by the lack of closure or the explicit promise to viewers that Team Rocket will definitely return to the show; the two-parter is merely considered to be Team Rocket's final battle in Unova. It is quite reasonable to assume that we haven't seen the last of Team Rocket in Best Wishes, even though it is unlikely they will return to Unova (as that would defeat the purpose of having them leave the region in the first place).
We also know that at some point in 2013 a chibi figure set of the Kyun Chara series will be released. It will feature James, Jessie, Meowth, Ash, Pikachu, Eevee, Lucario, Oshawott, Snivy, the first-stage Kanto starters, Charizard, Mewtwo and Mew; more Pokémon will be announced closer to release. As you can see, there is heavy focus on Generation I critters. We also know that Eevee will appear in the Unova League (which will most last until January 2013) and it is quite possible that Kotetsu's Riolu will evolve, too. But unlike Eevee and Lucario, the Kanto starters and legendaries aren't included in the current Season 2 poster or opening, which would stand to reason if they were to appear after the Unova League (at which point a new opening and poster are to be expected, although I don't expect to see a Season 3 labeling). I think that there is a very good chance that the Kyun Chara set will be correlated with the post-league saga of Best Wishes, meaning that Ash will return to Kanto and encounter Team Rocket, Mewtwo and Mew, as well as being reunited with his Kanto starters.
Now, the idea of a third Kanto journey does seem repetitive. But Unova is the only region featured in the current games, and there is really not much left to do with it after the league. While some towns were skipped (Aspertia, Floccesy, Lentimas, Black City and White Forest), Ash didn't have any reason to visit them in the first place. If the writers had wanted him to stay in Unova until the end of series, it would have made far more sense to leave East Unova unexplored, with the Junior Cup taking place in Aspertia or Floccesy. It's not as if the Meloetta two-parter necessitated going to East Unova, either, considering that the water temple isn't even based on the in-game Abyssal Ruins. About the only good reason to stay in Unova would be if the writers suddenly wanted to incorporate the Team Plasma story (in very little time given that they haven't even been introduced), but there is no evidence of that being the case seeing as it has been promised that Team Rocket will return.
As Ash's home, Kanto is the default region that the writers can turn to for a "filler" saga. Granted, they can invent their own region akin to the Orange Islands, but that's arguably creative hassle that they only opted to do in 1999 because they had just finished covering Kanto (the only game region at the time). For the Battle Frontier saga, the return to Kanto was arguably justified by FireRed and LeafGreen being recent games, but the writers didn't showcase any characters from those games (except for Misty and Gary, who would have returned regardless of the remakes) and the Sevii Islands would have been a better way to promote the remakes. In every saga, most episodes don't pertain to game locations or characters, so the post-league sagas can pretty much be set anywhere. In the same way that the Battle Frontier was moved to Kanto, so could the World Tournament cups, which would allow the writers to continue promoting the B2W2 games. This time, if the writers actually wanted to adapt the World Tournament more closely than they did in the Junior Cup, a return to Kanto would be ideal for showcasing some of the previous gym leaders. It is notable that an upcoming Best Wishes DVD set will contain all the Kanto gym episodes. In fact, most of the Best Wishes DVD sets contain Kanto episodes, and generally speaking, the writers haven't been shy about drawing parallels between Unova and Kanto.
As for Team Rocket, I'll be bold and suggest that their next plot may involve Mewtwo and Mew again. Giovanni's memory of Mewtwo was wiped out in Mewtwo Returns, but at least Meowth (and I believe also Jessie and James) wasn't affected. It would be interesting if now that the TRio are back in Kanto as Giovanni's lead henchmen, they were to remind him of Mewtwo's existence. It would be much more significant if Team Rocket's last mission in Best Wishes actually involved their history, which was an element sorely lacking from their Unova missions. At the same time, the writers would need to be careful not to be repetitive, considering that Mewtwo and Mew appeared together twice (although the last appearance merely involved their artificial counterparts) and were each given separate appearances. To make things different, it would be a good idea to incorporate Genesect into the arc. Since it is fairly obvious that the real star of Movie 16 will be a Generation VI Pokémon, chances are that Genesect's role will be relatively minor. The writers might want to compensate for that by giving it a role in the show, as they've just finished doing with Meloetta. In fact, its anime appearance could lead to Movie 16, as was the case with Mewtwo back in 1998.
While Team Plasma created Genesect in the games, that doesn't have to be the case in the anime. In fact, only a single scientist from Team Plasma showed interest in Genesect in the games, and the actual team never tried to use Genesect to faciliate their plans. In the anime, the scientist could either be replaced with Dr. Zager, or he could join Team Rocket under the reasonable assumption that Team Plasma has disbanded (but even in that case it would be simplest if Dr. Zager turned out to have originally worked for Team Plasma).