Team Rocket, for me. I was never able to take any of the other ones seriously. Maybe Team Plasma, to some extent, but even they seemed nuts.
TR was in it for money. They were typical thugs and mafia guys, not above harassing kids or strangers for their Pokemon. They worked both behind the scenes and out in the open and even in their disorganized state in GSC, they always seemed like a serious threat. They were analogous to the real world and they actually had power so they scared me.
Team Aqua and Team Magma? Uhh... okay. I guess they're based off of environmental nutcases but managing to get THAT many people to go along with what was essentially "hay lol let's get rid of all water on earth" or "land sux let's flood the earth". Riiiight. Their ideals were just so stupid and over-the-top that I could never take them seriously and they, along with all the annoying surfing routes, completely ruined gen 3 for me. I still roll my eyes when I think of them. I mean, it's one thing to be an environmentalist but trying to wrap my head around the idea that neither team stopped for a second to think about what the consequences of their actions would be? Eh. I just can't buy it.
Then Team Galactic was better than Aqua/Magma because at least they were fashioned after a cult and I could see that sort of thing happening, but somehow I still felt really disillusioned by them. I guess the idea of a cult that sounds so insane actually coming close to their goal just doesn't seem realistic to me. :( I will admit that this one might just be my own bias, though. People do in fact get roped into following weird apocalyptic things and I know some new age Japanese religions were seriously into this sort of thing, so I can see how it could come about. Couple that with Pokemon who can do the job and I guess that's pretty threatening. (I may have just convinced myself that they are a legitimate team while typing this out.) It still just sounds silly to me, though, so they aren't really in my rankings for favourite.
