Have you tried merging those scenes? Even if the format is structured and in plain text, it does not mean that a human can manipulate it as a patch. The format is so convoluted and full of magic numbers, it would require a lot of experience to really merge them; or support from Unity itself, and then the choice of serialization is not really that important.

You can manage team work somehow with prefabs. But I would like to see something like Havok Vision Engine's layering system, where every layer of a scene is it's own file, thus with file locking you can work on a single scene as a team. For example, you could split the scene in layers by developer, and then have someone integrate them in proper layers. Or you could just split specific work between people with lighting layer, static layer, collision layer and so on.