Both in A Very Potter Sequel and Me and My Dick, Nicholas Joseph Strauss-Mathathia's character leaves in the end of the play, and even uses the exact same piece of dialogue: "I could travel the world. I've always wanted to see Venice."
Actress Brittany Coleman plays Dean Thomas, who sounds just like Gary Coleman.
Luna Lovegood's cameo and explanation to why we don't see her in the original.
It's explained why Dumbledore was able to Dissapperate inside Hogwarts in the first Musical when Umbridge questions it after his escape — he never did, he just seems to say "Dissapperate" whenever he leaves a room.
Writer Revolt: It seems the writers/creators have mixed thoughts about their decision to censor and edit A Very Potter Musical to something worthy of a PG-13 once it caught on with younger audiences online. Though censored F-bombs and edits appear in the sequel too, Lupin and other new characters seem to been written specifically with Cluster S Bombs and similar frequent (but PG-13-appropriate!) profanity sewn into their personalities, and in a sly nod to the original censorship, the kid characters (now only eleven!) cover their ears anytime Lupin swears.
When the kids go back in time and they see themselves in the past, they're all played by people in the play who look nothing like them. Draco is played by the tallest guy in the show (Jim Povolo a.k.a Goyle) Hermione is played by a husky man (Richard Campbell a.k.a Neville), Ron is played by a much skinnier guy (Brian Rosenthal a.k.a. Seamus), and Harry is a petite Asian girl (Sango Tajima a.k.a. Lavender Brown) in an afro wig.
A second epilogue where Lockhart achieves his dream of being found by mice was not present, probably due to the fact that it makes the "writing of the Harry Potter series for Muggles being done by Lockhart" subplot not make a whole lot of sense.
Right after Hermione accepts Ron's proposal, Dumbledore and Rumbleroar made a cameo. There's no explanation as to why it was removed (if it was even in the live show).
Hermione's "transformation" being a result of using the repairo charm on her face when Neville broke her nose.
The Other Darrin: Meredith Stepien replaces Bonnie Gruesen as Hermione. In true StarKid style, it is immediately lampshaded. Hermione breaks her nose at the beginning of the musical and fixes it with a spell, but looks different.
Hemione: Well, I may look different, but you guys should just treat me like I'm the same old Hermione you know and love. (To audience) And that goes for all you too. (She winks at audience)
Throw It In: "I hope you find that swimming pool" in Harry's repeat of "Going Back to Hogwarts" to his son was added last minute back stage. And all the better for it.
The whole rule about having to touch the diary to see/hear Voldemort was something Joe Walker improvised to justify why Hermione couldn't see or hear him (In the script this isn't mentioned at all and he just hides under a desk when she comes in, but since this was a staged reading, there was no desk and thus, no real place for him to hide). And rather than treat it as a throwaway improv, Darren chose to bring it up again, turning a dramatic confrontation into comedy gold.