Mario with Lasers
Unfazeable
I doubt they will change the Team Rocket Storyline completely.
Maybe just tweak it a little like in FireRed and LeafGreen.
Out of curiosity, what were the tweaks TR had before the Sevii Islands in FRLG?
Wait a minute... I know Anime=/=Games, but the intros to one of the movies features Rayquaza inexplicably captured by Attila and Hun (Team Rocket in Johto), which could, possibly, maybe, not very likely, have a tie in to HGSS?
I dunno, I kinda doubt it, but could be a way to tie in Groudon/Kyogre/Rayquaza.
They don't need to tie the weather trio. If they want to add them, they could just use Navel Rock (NOT the Sevii, only it and maybe Birth) and make it an event-only island, just like it was last gen for Lugia and Ho-oh.