In my opinion this list sucks. It would be much better if it was broken down into original screenplays and adapted screenplays.
Original screenplays should automatically rise to the top of the list. I'm not saying that anyone can adapt a screenplay, but most of the hard work has already been done; beginning, middle, end, plot, characters, character development and in many cases a built in audience who already care about the story.
For example Fargo, number 32 on this list, in my opinion should be ranked higher than The Godfather, which comes in at number 2 on this list. Joel and Ethan Coen wrote the screenplay as a completely original work for Fargo. On the other hand Francis Ford Coppola had the existing novel and the help of Mario Puzo, who wrote The Godfather, to mold into a screenplay.
You have to give credit to something that is 100% original.
As a disclaimer I am not saying Fargo was a better film than The Godfather, quite the opposite. I'm just giving my opinion strictly based on screenplay.