Really I wouldn't call Lavos a villain. He's more of just the main conflict or a really powerful monster honestly. He doesn't plot, and he doesn't do anything evil, he just flies around and looks for food like any living thing would, it just so happens he eats planets.

possesses an intellect FAR above any other living being
I don't seem to recall them ever showing or implying that Lavos was more then a mere animal working on surviving.