I think Team Magma is better based on their goal of expanding the land, while Team Aqua is better because they had Kyogre. I just can't take Aqua seriously on their own. Imagine if they won!
"WE DID IT! WE FINALLY EXPANDED THE SEA!"
"Yeaah...you expanded the sea and now there's almost no land where we can live on."
"But now we can live underwater! In cool bases! Or on boats!"
"And just WHERE are we going to BUILD those bases and boats?"
When it comes to the legendary, i prefer Kyogre over Groudon. Love Kyogre's design, plus his Drizzle + Thunder combo make him a very dangerous opponent. When it comes to design, i think Magma has way cooler outfits than Aqua, i didn't really like their sailor themed uniforms.
So if i had to chose a Team, i'd got to Magma...i would probably end up being a simple grunt, thus i wouldn't get to have the legendary, so at least I'd have the cooler clothes