Jonathan Blow wrote an excellent article on the text-based entity file format he developed for The Witness, which was designed to be (more) mergeable:

http://the-witness.net/news/2011/12/engine-tech-concurrent-w...

That was a great post!

I am legitimately surprised they're using a binary format for scenes. That is very anti-source control in general. The only binary blobs in the entire project should be assets (e.g. textures, sounds, etc). Everyone loves to whine about XMl, but I'd happily take XML for scene layout over a binary blob.

By default it is binary, but you can change it to a textual one: http://docs.unity3d.com/Manual/TextualSceneFormat.html

And they've also improved the merging story, see: http://blogs.unity3d.com/2015/02/17/production-workflow-impr...

Scenes and prefabs have been able to be saved in a text format for a while. That said, they were still effectively unable to be merged in all but the simplest of situations for reasons I don't fully understand.

Hopefully this was improved in Unity 5. One of the buried release notes mentions a new merge tool for scenes and prefabs in the engine.

Binary scenes are optional. Text format scenes (similar to xml) are better, but still not easily merged.