Cut Song: Many songs from 1.0 were altered or cut, such as the opening "Splash Page" number. Arachne's songs got hit hardest; she lost "Deeply Furious," "Think Again," "Love Me or Kill Me." Some lyrics from "Deeply Furious" were reused in "A Freak Like Me Needs Company."
Drawing Board Hiatus: Came with the Troubled Production. The script underwent several reworks, Bono and The Edge from U2 were brought in to write new music, original director Julie Taymor either quit or was fired after rejecting the changes from said reworks and the musical had the longest preview period in Broadway history with an astonishing 182 performances before the official premiere.
Lying Creator: Videos and statements before previews began claimed that the musical was "based on the comics, not the movies." It's actually a composite adaptation of Spider-Man and Spider-Man 2.
Recycled Script: The first version had quite a bit of dialogue from the first movie in it. The second got rid of most of it, but scenes like Spider-Man saving a baby from a fire still seem directly lifted.
Oddly enough, the Green Goblin is given the backstory of Dr. Octopus from the second film, with Harry Osborn not existing at all.
Troubled Production: Quite possibly the most infamous, noteworthy and widely mocked example of one in Broadway history. Find out more here.
Originally, Evan Rachel Wood and Alan Cumming (both of whom have worked with Taymor before) were cast as Mary Jane and The Green Goblin, but the endless delays the show faced getting to the preview period led to both dropping out.
The original plot didn't have Arachne function as Peter's Spirit Advisor, but had the actual Arachne from the Greek legend as the Big Bad rather than Green Goblin, with Gobby getting killed off at the end of the first act. Arachne was also the leading lady. She had a song about trying on shoes and a very blatantly Foe Yay-laden scene where she sneaks into Peter's room and sings Turn Off the Dark. She also had two master plans, either of which she would have been perfectly fine with: either have Peter fall in love with her, or have him kill her. Either way, she's freed from her curse.
After it's closure on Broadway, there were talks that it would be revived either as a tour or a permanent show in Las Vegas, but nothing has come from this.