Giovanni, cause he's the classic villain. I loved it that he returned in Fr/Lg, and now he's got a more complex personallity (with Silver and all). It isn't an excuse for all the wrong things he did, but at least he wanted to do something good with capturing Deoxys. Now is Silvy reunited with his father ^^ (If he'd wouldn't be a statue anymore..)
Second is Marge / Courtney. She's cool and strong, but she also has a soft side. I loved the interaction with Ruby and her, and it made me wonder about their relationship. If Ruby was only a bit older... Na, anyways, Marge is now happy with watering her flowers ^^
O, and I totally loved the Elite Four for being these awesome strong villains (instead of being the good guys as in the games and the anime). My only complaint is that Lance looks like a kid. Please, why couldn't he be drawn a bit more... manlike?! It looks kinda silly when he commands his dragon pokemon and he has the body of a kid. Ah well. The rest of the Elite Four kicked ass, with merciless Lorelei (pity she lost her personality in Fr/Lg) and Agatha 'with her grudge against my grandfather' (Quoting the ever so lovely Green ^^)
