Pokemon Black and White 2-Now with a sexy rival.

Not at all, team aqua hated people for polluting the waters so fill the world with water get rid of land dwelling people problem solved. They were motivated by their love for water pokemon. Team manga on the other hand wanted the land for more space for people and pokemon to roam about. The underlying issue would be overpopulation so they decide lets tap into all that land a the sea floor.

N just want pokemon to be completely free of people.

That was the point, N would be against both Team Magma and Team Aqua