And triggering Nihilus' introduction takes longer. Obsidian really didn't want you to remain neutral. I can see why considering the game design, I guess.
But two recurring themes were that everyone sees Jedi and Sith as the same, and the True Sith are so bad that both sides will want to destroy them, and may need to join forces to do so. So I'd say neutral could bring an interesting perspective. Kreia was neutral and she got to be a powerful Force user.