I'd choose Magma.
Copypaste incoming.
Maxie was an industrialist with several legitimate avenues of wealth. Mining, landscaping, real estate, agriculture. He wasn't a geologist, meteorologist, or environmental scientist - he didn't fully understand the breadth of Groudon's power. However, he understood very well Hoenn was mostly water with burgeoning populations ready for expansion and resources to extract. Groudon would increase the landmass, allowing for great profit. Having the volcano erupt right over the desert to the east, would make the land very fertile and expand agriculture, and the emptied volcano could be more easily harvested for resources. He was a businessman manipulating mostly deluded fanatics.
Archie is similar - he's clearly just a pirate, albeit a very talented one. He can pilfer and pilot a submarine and is much more successful at raiding companies like Devon than Magma. Since Aqua is based on maritime thievery, expansion of the sea increases a reliance on sea industries and sea travel, making it easier for Aqua to raid ships for goods.
Aqua and Magma are criminal organizations fronting as eco-terrorists. Archie and Maxie recant their advances when they understand how destructive and uncontrollable Kyogre and Groudon are - as businessmen, not historians or environmental scientists, it took an apocalypse to make them see past their greed.
