Seems like this thread quickly became about problems people see that they feel have yet to be fixed. It was an interesting opening question/topic, so I hope other people have ideas on already-fixed problems.
I'm not sure if people would consider this fixed or not fixed - or even a problem - but I would like to see an exploration in-story of the personality/philosophical changes that happened from Ditko-Spidey to Romita-Spidey. Has this ever been directly addressed? I've given a lot of thought to what I might do if I was ever living in a dream world where I got to write Spidey long-term, and this is something I've considered tackling.
Similarly, I'd love to write about how Peter Parker isn't actually all that responsible, despite appearances.
-Pav, who would utilize Flash-Venom a heck of a lot for that...