What I see happening is that the next game has Giovanni return. He's still around somewhere. He's an iconic character in a way none of the rest of the villains have been. There is so much to work with there. Why waste it. Every gen has had a game with Team Rocket, 5th gen should too.
Which is pretty much why I'm tired of Team Rocket and Kanto, They've been done to death in every generation. It's time to move on from them. The TR in the anime's still fine, but in the games... it's just tiring. They were beaten in RBY, brought back in GSC, we re-beat them in FR/LG, and re-brought back and defeated in HGSS, along with Kanto. After playing all of those games save one (SoulSilver)... I've pretty tired of that, and would like to just put it behind me. They were all fun, but that's really enough for me. Team Rocket was introduced, defeated, attempted to be reformed, but failed, and defeated again. Anything more with them would pretty much just be a repeat of what's already been done, most likely of Gold and Silver's plot, and thus, at least I'd prefer to just have some new team again than to entirely reuse already existing game's basic plotline.
As for Giovanni... I wouldn't mind a small cameo-type thing with him somewhere, similar to the event in HG/SS and continuing where it left off, so long as he doesn't bring Team Rocket with him. I mean, there's a reason the guy didn't actually show up to help TR in the plot of GSC... And the
Celebi event helps elaborate on that: he was planning on helping them, but after being beaten by Lyra/Ethan, repeating his defeat by Red in the original games, his mind began to shift, and he realized that the dream of Team Rocket was just an illusion. That's why he doesn't actually show up to help. Him changing again and actually resurrecting TR/helping out a resurrected Team Rocket would just be weird after that--he didn't help TR out in Johto, but he helps them here? That's just weird...
Although... thinking down that line though gives me an idea for a Rocket-based plotline I wouldn't actually mind, as a true conclusion to Team Rocket, once and for all: the Grunt does end up going to another region, and manages to get a small following there. As the player of course, you have to stop this and set out to defeat them. While you're doing this however, you join up with a mysterious person who also seeks to make it to make it to the head of this new Team Rocket faction, and helps you out in a Double Battle or two along the way (think: the way Lance helped you out in HG/SS and such). Eventually you make it to the head, and defeat him. However, he still doesn't give up, and is prepares to take drastic methods of some sort. That's when the mysterious man shows up again, and reveals himself to be Giovanni, the original head of Team Rocket. The new head naturally recognizes him and such, but then recalls how he was helping the player to defeat some of his minions, and is confused. That's when Giovanni explains that being defeated by Red bean to cause him to rethink thinks a bit and try to become stronger, but being defeated by Hibiki/Kotone made him realize that Team Rocket was from the beginning a futile endeavor, doomed to be defeated by people with true strength of Heat and Soul. After he finishes his speech, he leaves, and the new Head Grunt surrenders.
I suppose if it ends up going something like that, and gives true closure to the Rocket storyline, then I wouldn't mind it, especially if it was somehow worked out to be more of a post-game plotline and not the main focus of the games themselves (like, something slightly different from the above: after you beat the Elite Four, you'll shortly get a call about the grunt taking over that region's Radio Tower with a small group of followers or something. You go there, beat up the lackeys, and end up teaming up with a Mysterious Man to take down the head guy along the way. After the fight, the Mysterious Man reveals himself to be Giovanni, and it continues from there). But if it's just a re-hash of G/S's plotline through and through, especially if they throw Giovanni in there as being wholly evil and behind Team Rocket, I could do without it.