How would you fix MCU Spider-Man?
Spidey becomes a SHIELD agent. Nick Fury managed to shut down the Peter/Spidey angle by using LMD-clone of Peter, code name Scarlet Spider.
While Peter is doing secret ops, Scarlet Spider steps in for Peter. However, Not!Peter managed to alienate themselves from Pete's friends. Aunt May goes prematurely white haired from the stress.
Bring in actual MJ, the sexy ginger, not the scruffy mixed girl. MJ is actually Peter's combat instructor, her parents were SHIELD agents but were killed by HYDRA. Not!Peter develops into his own man. By end of the movie, Not!Peter becomes Ben Reilly and goes his own way.
Ben's villain is the King Pin. Having learned about Peter, Kingpin seeks revenge. The end fight would be Ben v Black Cat while Kingpin gets away with everything,
Mid credits we see Oscorp & Kingpin are in cohoots. Together they'll make the Sinister Six.