Not to mention, it being text, it should be a lot easier to copy and paste data from one map to another. In theory, you will be able to load maps within other maps without compromising instead of the limited prefab system in LE4. It would be like how prefabs work in Hammer. You should be able to store flowgraph data in it too.
A tad worried on the speed cost as this is the first time I heard you planning on something that doesn't prioritize speed. I would do benchmarks to see how slow this might be.
Whatever you decide, I'm looking forward to seeing what you come up with.