The only system I know of that truly tracks changesets rather than revisions is Darcs.

But from a more practical standpoint, tracking changesets rather than just revisions means recording ancestry ("commits also have other commits objects listed as their parent commits") such that you can freely create merge revisions and the system will Do The Right Thing with minimal hand-holding.

The internal repository format isn't really relevant here, it's about the way of thinking that the system is designed to support.