I made my own evil team from Hoenn.
You're obviously aware of Team Magma, who wishes to use Groudon to expand the land, and Team Aqua, who wishes to use Kyogre to expand the sea. If you've been on Pokemon YouTube, you're probably also aware of Team Sky, a third team who wishes to use Rayquaza to expand the sky...whatever that means.
But those three are not the only teams from Hoenn. There is another.
Frankie is the leader of Team Flora. Unlike with Maxie, Archie and Mikey, Frankie puts up a goodhearted front to make herself appear as a trustworthy woman with a simple goal to bring more nature to the world. But deep down, she is devious and psychotic, and more evil than the other three team leaders put together. She doesn't just simply wish to bring more plantlife to the world - she wishes to BURY THE WORLD IN PLANTS, FLOWERS, TREES AND EVERYTHING ELSE, probably leaving humans and several Pokemon to suffocate underneath the endless waves of spreading plantlife. She is also deeply nihilistic and misanthropic. She despises humans and almost all Pokemon, seeing them as terribly flawed and unworthy of the perfect world she wishes to create. As a result she feels no guilt and shame in committing terrible acts all in the name of furthering her agenda.
And as for her plans for the Legendaries? Well...her hatred expands to the three Super-Ancient Pokemon. She despises all three of them and the teams that worship them, seeing them as beings that have corrupted the world from the state she wishes it to be in. So instead, she is seeking the mysterious Grassland Pokemon Virizion to use it to usher in an era of nature - and, in the progress, she wishes to KILL THE THREE SUPER-ANCIENT POKEMON.
Lysandre with extra steps? Maybe. But I like this idea nonetheless. Now if only Tropius had a Mega Evolution...