I may be a bit biased here, but I've always way preferred Team Magma. I definitely like their costumes a lot over Team Aqua's, simply because they just shine so much more of badass, whereas Team Aqua's has always come off as pirate costumes to me, and I've just felt like that was really unfitting for whatever reason. I think Team Aqua become a lot cooler in the remakes, but for the originals, Team Magma definitely takes the cake when it comes to the costumes. I also really like the mixture of red and black over blue and white, so there's also that.
There's not a huge difference when it comes to Pokemon. In general, I actually usually prefer Water types, but I feel like when it comes to evil teams, it's more about the coolest Pokemon, and the Fire types are definitely have more of those. Water types are usually more elegant in their designs, even though Sharpedo is one of the exceptions. But yeah, their Pokemon are mostly the same, apart from the Camerupt/Sharpedo. Between Groudon and Kyogre, I've always preferred Groudon as well. Kyogre is definitely the strongest of the two, but I've always heavily preferred the design of Groudon. Its name sounds so much more menacing as well. That's not to say I don't like Kyogre though, I've just always preferred Groudon between the two.
And lastly, I also prefer Team Magma's cause honestly. Looking from a real world perspective, I definitely wouldn't want either of them to go through, but I would be lying if I said I didn't think Hoenn could use less water. I've already mentioned in the Deoxys Challenge how much I dislike the amount of water, and especially in the third generation games where the repels are so incredibly expensive. So for Magma to create some more land to walk on wouldn't be the end of the world for me 8D
But yeah, that about sums it up. In general I feel like Magma outshines Aqua on so many levels, though a lot of this is leveled out in the remakes, especially since they also factor in the personalities of the two leaders (even though I still prefer Maxie there 8D). But again, like I said, I'm kinda biased due to Ruby being the version I first got and played through. My opinions might have been different if I'd gotten Sapphire, but that wasn't the case :D