I'd join team "We're bigger than a 10 year old kid, so even if he wins the Pokemon battle he still won't derail our entire world corporation."
I don't know if this counts or not, but Team Galactic didn't disband after the player caught Dialga/Palkia. Well, not entirely - Saturn was left in charge. Most of the grunts left with Cyrus, Mars, and Jupiter, intent on continuing their plans.
Anyway, out of those (what does Other mean? You mean little 'organizations' like Phantom's or even Hunter J's?) I'd probably join Galactic. I don't care much for my looks, so sacrificing my hair to an aqua bowl cut (a wig, perhaps?) and walking around in a jumpsuit wouldn't matter much at all to me. I see eye-to-eye with Cyrus on some things. Plus, running around the HQ via warp panels would be awesome. Sure, the Pokémon the grunts have ain't that great, but just
being around those people would be great fun. I mean, come on, the subordinates were epic in the games. EPIC! Aah...I could go on, but...
Team Rocket never really interested me. Okay. It's a crime gang. Who, in the anime, wanted to take ova teh world. Sure, they had grand technology and a few great accomplishments (creating Mewtwo and taking over the Silph Co. building, for the most part), but other then that...I don't know. They weren't anything new for me.
Team Magma and Aqua...sure, they had the coolest uniforms, but honest-to-god, I don't think I will ever find anyone more dim-witted and delusional than them. Flooding the planet? Turning it into a giant desert? I just, ju---...gosh, I have nothing to say.
Team Snagem...uh...they're the guys who turned Pokémon into a Shadow form, right? I haven't played Pokémon Coliseum.