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Well, I sort of expected Team Rocket to be winning. I don't know why I don't like them. >.>
Well, plot wise my favourite is definitely Galactic. They might be a little extreme and dress really weird, but I have a respect for evil groups that get stuff done.
1. They were difficult when I was a kid, as opposed to Magma/Aqua, who were easier to stalk.
2. Hate Galatic, can't even remember anything about them.
3. Rocket's been around forever.
Plus beating Team Rocket means more to me thanks to the anime than beating any other team. I assume Plasma will be awesome though.
I'd say the rockets are my favorite. I just liked the way that they went about accomplishing their goals in HG/SS.
Team Galactic was OK in my eyes, but they seemed a bit TOO powerful and organized, I just didn't like that.
I like Magma and Aqua as well, their evil plan to eco-terrorize the Pokemon world wasn't all that great, however.