I've often thought a chamber-style musical focusing on Ultimate-styled Mary Jane, Gwen, Aunt May, Spider-Girl (a clone of PP, but, y'know, a chick), and Peter would be affecting. Green Goblin would be a good villain, but not in the Ultimate fashion where he is a giant Hulk-like creature.
A better musical villain might beeeeee, ummm, Doc Ock? His backstory, outside of the Ultimate books, often has the pain suited to an opera. Ultimate Venom, where the creation of Venom is tied to the cancer research of Peter's deceased father, would make for a promising musical.
No one should adapt Spider-Man without becoming familiar with Bendis's take. From what I recall Taymor did not get past the first page of the first issue where Arachne is briefly alluded.
With Irma you gotta do something!