On the subject of long super hero campaigns: if you have never read it, I highly recommend Aaron Aalston's Strike Force. It is a Hero/Champions specific book, buy the important parts are completely system agnostic. Allston manage to run a long term campaign with multiple groups and solo heroes, embracing the very Bronze Age interpersonal conflicts and melodrama of the era. It is a master class not just in running a long term.supers game, but any long term game.
I do not own nor have read the more recent update, which includes a lot of essays by other supers RPG luminaries, if I understand it correctly. At the time of the Kickstarter, I did not believe one could improve upon AASF. But one of these days I should grab at least the PDF.