I bet they changed:
Hal's backstory - Hal's backstory for leaving the Air Force and becoming a private test pilot was changed in the 1° draft. I'd say that Johns might have added a tweaked, yet more faintfull version, in the 4° draft.
Abin Sur's spaceship - It has been comented that the writers used John's version of why Abin Sur was using a spaceship instead of the ring. It actually fits the story and it's better than the original reason they used.
Hector Hammond - This isn't as much a bet as it is a wish. Johns fleshed out Hammond amazingly in the comics, making him a psycothic telephat who feeds of other people's memories and emotions. It'd be something interesting to see in a movie, besides, it'd flesh out Hammond's kinda contreveid character from the 1° draft.
The Emotional Spectrum - The Emotional Spectrum alredy appeared in the 1° Draft, but in a tweaked version. With Geoff's revision, I bet the Spectrum will appear in it's full glory. Maybe even foreshadowing the War of Lights.
Nipticks - I think they might also have changed the 1° draft's nipticky mistakes, live inverting Hal's brothers ages, changing names, merging characters and etc.
How about you? What do you think they changed?