My guess for
Paradise, the movie they skipped.
David and Shaw arrive, get involved in conflict between good and evil Engineers, movie ends with David destroying Engineers.
Similar to what we got but the first part would be shorter. Less time on the ship and problems occure faster after landing.
More time spend on David and his gallery (bigger in early draft) and on his secret room with Shaw drawings and experiments (also in early draft).
Perhaps Advent style flashback once David gets busted, actually showing what happened to Shaw. David unleashes his creatures (shown in concept art).
From here everything else might have been the same or similar.