Okay, I put on my nitpick hat and tried to think of a few things that have bugged me over the years... warning: obscure continuity ahead.
What was up with Looter's mysterious meteor thing from the Sensational Spider-Ben days?
What happened to MJ's sister and her nephews? They kinda pulled a Chuck Cunningham and just vanished.
If Alison Mongraine didn't have Baby May in the cart she wheeled outside to Norman Osborn at the end of the clone saga, then just what the hell was it and the "delivery" she talked about and why was she wheeling it out of the maternity ward? (again a testament to how awful the hasty rewriting to make the "package" Aunt May was.... thanks, Byrne)
Whatever happened to the gold note-pad Peter lifted from that building the Beyonder turned into solid gold? How come he never cashed in?
What is Mysterio's status? I haven't understood if he's alive, dead, what, since he returned after blowing off his head in Daredevil.
How did Morlun come back after being turned into green powder at the end of JMS's first arc? That was never really explained. He just got "better."
How does Peter know he's the REAL Peter Parker, just because Ben Reilly wasn't? And why did Reilly degenerate when perfect clones weren't meant to?
Wasn't the Vulture... and Eddie Brock... and I think Cletus Kassidy all dying of terminal cancer at one point (that seemed to get swept under the table as new writers took over)?
I could go on, but now I'm going away from unresolved plots into nitpick territory.
