What I was getting at is mainly world building,
If it's the dawn of heroes type story, then the narrative should follow heroes only. Kind of like the golden and silver age comics.
All the more convoluted story lines in which villains became main characters and such were best told after the world/campaign setting was already established, because now the narrative changes the accepted in-universe rules.
At any rate, your initial post already says heroes and villains have been around a while, so it's a moot point. Heroes and villain team ups for the win.