speaking of bleed over... maybe have Pete's organized crime foes throw in with some of the other criminal elements in the MCU. For example: Stane's operations weren't exactly legit, maybe he contracted some things through mafia types?
I think that works for a thirty minute TV episode, or a two issue comic book story, but not for a two hour film.
It is worth noting that there has been some bleedthrough. Part of it is that Peter worked at the Bugle (although that was an era in which teens had responsibilities) and had the likes of Captain Stacy in his social circle.
The Big Man turned out to be one of Peter's coworkers. Betty's brother turned out to be a gang lawyer. The Kingpin kidnapped Jonah in his first appearance (and was responsible for the death of one of Peter's coworkers.) He kidnapped Gwen and Captain Stacy in his second appearance.
The Ultimate Spider-Man story "Learning Curve" (one of my favorite Spider-Man comics ever) had Peter decide to take out the Kingpin after learning that Uncle Ben's killer was connected to him. In the Ultimate comics, Peter was outraged that people knew that the Kingpin was a criminal, but he was allowed to walk free. It's a hard needle to thread, but it is doable.
Sincerely,
Thomas Mets
I think it depends how you work it, because there've been several major crime boss characters who have had no relation or connection with Peter.
Peter's life entwining with Spider-Man is common but it's also common where they run concurrently, if not actually intersecting.
(But I don't count a crime boss kidnapping someone Peter knows as on-the-level as one that personally knows who Peter is).
I'll note Peter's life entwining with Spider-Man's doesn't require the bad guy knowing his secret identity. For instance, Robbie Robertson had a connection to Tombstone that connected the new villain to Peter's life.
There aren't that many good Spider-Man crime stories where there isn't some kind of connection to his private life. I guess "Spiral" focused mainly on the story of a side character. With the Owl/ Octopus war, the Black Cat was seriously injured, and Peter visited family and friends before he thought he would have one of his biggest fights ever, but part of his arc was about how Peter Parker's loved ones didn't know about what else was going on in his life.
Sincerely,
Thomas Mets