A second thing I just found out, it seems like while the Sepulchre fix works great, everyone's working just fine there, something still causes issues with the Stygian Abyss section (the actual Mephisto bossfight level). With one combination of characters (Iron Man, Spider-Man, Batman, Superman) only the last character had powers and only some of them worked, while with another combination (Batman, Ghost Rider, Stan Lee) the game just sat on the loading screen and then froze.
My hunch is this is due to the 117 fightmove limit that still exists?