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But because your question only asks about Magma and Aqua, I'll have to go with Aqua. I'm fond of the colour blue. Plus I have no tolerance to heat at all. And I'm a fairly strong swimmer.
I've been told I'm a 'lil fish..well not anymore, now I'm quite a big fish xD
Since I'm into diving (Scuba not the one of the boards), so more water would be nice. Plus Blue is a better colour than red, 'tis a fact.
Aqua is awesome because Kyogre and the sea is awesome.
Land is awesome as well, but Groudon is not as awesome as Kyogre.. imo
Team Rocket is lame (NO NOSTALGIA FROM ME HAH!)
Team Galactic is even lamer.. basically Team Rocket with Glameows and Stunkys instead of Rattatas with stupider outfits.. >.< Glad i'm done with them again :)
Rocket for being genuinely criminal an' all. This has been said before many a time by the older folks here etc etc etc.
If you want just out of Aqua and Magma though, I'd say Aqua because they look like pirates... and yes, pirates of the golden age did look stereotypically like that, they just didn't say 'arr' all the time.