1. He Was Going To Scar Harvey Dent When On Trial In The Third Film
One of the big differences between Goyer's original plan and the final story is that Harvey Dent doesn't go through his hideous transformation until the third movie, in something that now reads as a mash-up of the villain's comic book origins and the version of events seen in The Dark Knight. After being captured at the end of film two, film three would see Joker on trial, during which he douses Dent with acid, sending the DA into a downward spiral and becoming Two-Face.
Although it's much more in-line with the comics, having the dethroning at the hands of the Joker means that the overarching impact - he's unveiling Gotham's dark heart - is similar to The Dark Knight's warehouse explosion.
A two-parter clearly doesn't fit with Nolan's sensibilities, so it'd be easy to conclude that the planned story was simply compounded down into one film, but the courtroom setting (which is homaged with Dent's introduction in the film proper) reveals the early script was very different from the finished movie.
And that seems like a good thing. Having Joker involved in Two-Face's origin so obliquely is the sort of happenstance meddling that dominated the earlier movies (Two-Face killed Dick Grayson's family, really?), something that really goes against how forward thinking The Dark Knight, and Heath Ledger's Joker in particular, was.
Were there any other ways Heath Ledger's Joker almost turned out differently? Share them down in the comments.