First off, Giovanni will have nothing to do with Team Rocket in HGSS; he quit the organization and wandered into the mountains to train. He has nothing to do with them anymore.
Secondly, I actually like Team Rocket a lot more than Galactic because not only are they evil, but they're more believable. I mean, a huge underground crime syndicate that uses pokemon as tools in their slow quest for dominance? I could see that. A huge group of idiots working for a huge multimillion-dollar company whose leader has all of a sudden decided to take over the universe? Pretty epic, but godawful if you really think about it. I mean, if there's any form of government in pokemon, or law enforcement or anything, why are they not doing anything about Team Galactic, who has the biggest freaking buildings in the country, stealing everyone's pokemon? That's gotta be illegal; the Elite Four should go in and deal with something like that. But do they? No. They leave it up to some kid to deal with it; hell, Cynthia KNOWS what Cyrus is planning, and does absolutely NOTHING about it.
As far as Magma and Aqua go, they're both jokes. "We're gonna make more land for people to live on!" "No, we're gonna make more water for pokemon to live in!" "But then the people will all drown!" "But if there's too much land, then the pokemon of the sea won't be able to survive!" "Then whatever shall we do?" How about LEAVE EVERYTHING THE HELL ALONE?! Nature's fine as it is; Archie and Maxie are just the stupidest idiots ever, and the only reason why they got anyone to work under them is because all of their Admins are totally batsh** insane and their grunts are too scared of said Admins to do anything but ask "How high?" when they're told to jump.
I think that Giovanni's really the best out of all of them; he was the strongest trainer in all of Kanto outside of the Indigo Plateau, and actually has some decent character development. Cyrus wins "Most Diabolical", but isn't as good as Giovanni; even after his ultimate defeat, he's still a douche. Archie and Maxie come in dead last, as they're just totally retarded environmental terrorists with absolutely no idea about how nature works.
I just hope that the Rocket Admins in HGSS make decent villains...