During the rough cut screening everyone felt it all worked until Marcia spoke up and said there was a lack of emotional resolution because Marion disappears, she's presumably left on some island with a lot of melted Nazis. So they filmed a new scene in San Francisco for the ending where Marion is waiting for Indy outside the building and Indy comes out saying they're all fools and they have some dialog and go off together. Its a small change, but a very effective one.