Basically it's a question of whether someone prefers them as a villainous team or as an organization
If someone views them as an organization, they are more likely to go for the following:
-Cooler uniforms
-Pokemon types used, including legendary "mascot"
-Hideouts
-Bosses
If they are instead viewed in regards to their villainous aspirations, you could look at their goals in addition to the other aspects:
-Magma undoubtedly had a more logical plan from the humanistic perspective, as it would be ridiculous to assume all humans would take to the seas in Pacifidlog town style should the oceans be expanded, whereas land expansion makes more sense, especially in a region like Hoenn with such a great amount of oceans already
-Aqua had a more villainous plan, or at least one less beneficial to humanity, however if you are feeling particularly misanthropic you might consider it an ideal plan
-Both sought, or claimed to seek new homes for Pokemon, so any PETA group in the Pokemon world would likely have supported them equally
So your options are pretty much: Which is better?
-Magma because X is cool/awesome/etc.
-Aqua because X is cool/awesome/etc.
-Magma because they had a more reasonable plan
-Aqua because they were more villainous
-Aqua because screw humanity
-Both are equal
My response: Magma because they had a more reasonable plan
Sorry to anyone annoyed by the long analysis