Yeh on the DVD there is a longer fight scene with the "Wave serpents" (i think thtas there names) and a few minor censors are removed

There is some extended stuff depending on if you watched the OAV or the actual movie.
There is some more stuff with Dorothy and all that.
Also, it was a point made in the movie, and OAV in the original Japanese, that they didn't kill any of Mariemaia's followers. At that point, they weren't out to kill, just stop the destruction her forces were causing. Everyone was tired of killing, highlighted by Heero's comments on how many more times does he have to kill that little girl and her dog.

I know that there has to be more because i have seen scenes of Dorthy and stuff that was from endless waltz but wasn't on Toonami. A lot of people say just get the DVD because it has everything. However i havent seen it soi guess that's not too helpful.

Do you have it in Japanese or in English?
English Language Anime: Dub it, don't pervert it.

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In the toonami version, they make a point of saying that they pilots deliberately fought of the bad guys mobile suits without killing anybody. Was that part of the original movie? It kind of sounded out of place.
English Language Anime: Dub it, don't pervert it.

I don't think the edited verison is that much different. maybe some blood edited out and some mild dialogue edits but other than that.
It's still the same movie.