I had Sapphire, so I saw Team Aqua and Archie first. Than when I got Emerald, I saw both teams. I was surprised to see Archie/Team Aqua take the more friendly side (though still bad), as opposed to Maxie/Team Magma who just didn't seem friendly at all. So Archie/Aqua takes it here, most likely because he was the main bad guy I saw first, but I loved how he had changed slightly in Emerald (I didn't have Ruby, so I never saw him trying to stop Maxie/Magma as the good guy).
The themes when talking to a Magma/Aqua member before battle. I just always liked Aqua's theme better, possibly because I'm more use to it. But Magma's, I dunno. Just didn't get the same feel for it, or like it that much.
Clothing. Archie's clothing over Maxie's. The bandanna really suits Archie's clothes.
I can't say the same for Aqua's design though. I just don't like the pirate look they don, even if it suits the water thing they've got going. But I lovvve Magma's clothing. The hoodie is just epic!
I do like Kyogre, but there's just something about Groudon's design I just love.
Overall, I like Team Aqua/Archie over Team Magma/Maxie. But there are some qualities of Maxie/Magma I prefer over Archie/Aqua.