I don’t particularly read superhero fanfiction. The never-ending, always-continuing nature of American comic books makes it difficult to write meaningful stories, since the canon is constantly shifting. However, alternate universes work very well in fanfiction.
One story that uses the alternate-universe idea very well, in my opinion, is David Golightly’s What If Spider-Man Had Been a Villain .
It’s framed like an old What If? issue, and it runs with the premise a bit faster than it probably should. But considering it’s a one-shot, the pacing is understandable. As an origin story, though, it works—and it works really well.
It even predates Superior Spider-Man by a few years.
Recommended if you like the character and don’t mind different takes on the mythos.