Have you heard of patch-theory-based VCS systems (Pijul is unstable, I heard Darcs is slower)? Instead of a chain of independent states (commits), each state is a set of patches (some of which depend on others). Pijul stores an internal structure that's more complex than "a series of chars/lines".

This eliminates complex rebasing topologies, and Git not recognizing that old and rebased commits are the same. But I'm not sure if it works well in practice. And it doesn't extend to SQL data sets yet.

I don't know if you're interested in this or not, but I just wanted to mention it.