Are you familiar with Bioware's games (Dragon Age, Mass Effect)? Because of the many different plot choices the game offers, a player might well find themselves returning to an earlier save-point and repeating a scene for the sake of picking a different dialogue option. I'm not sure this is what you plan for your game, but it sounds close enough.
In order to prevent the repetition from becoming boring, at the pressing of a button dialogues can be skipped line by line, until you get to the point of interest, and cut-scenes can be skipped entirely. This way, players do not get annoyed with the repetition. (Actually, there were some problems with this in the earlier games. They learnt from experience. You - learn from their experience; make sure that if there's a hard battle straight after a dialogue / cutscene, there's an opportunity to save after the scene, before the battle. So that a player who keeps failing the battle won't have to go through the dialogue again and again and again.)
Automatically skipping scenes is something I would not recommend. A player might enjoy replaying a particular scene, much in the same way one might enjoy rewatching a film. The issue becomes even more pertinent if the scene plays out with slight differences because of previous choices - players would enjoy looking for those slight differences, seeing how what they do matters. If a player doesn't want to watch the scene again, well, they have the skip option.