I don't know of a VCS alone dedicated to Model, because Model-base design is often part of a all chain of documents that need to be kept in sync.
Namely (not an exhaustive list):
- requirements documents (from which you start modeling)
- source code and documentations (generated and implemented from the model)
Plus, I never saw the GUI aspect fully solved in those tools (one model painstakingly organized a certain way might be versioned without layout information, and restored organized another way).
One tool I know of which covers all of those development processes is Modelio, which includes a "teamwork manager"

Another example (which I don't know as much about) would be metaCASE, which has an interesting paper "The Model Repository: More than just XML under version control", about DSM (Domain-Specific Modeling).
DSM: model-based software development approach that uses visual models as primary artifacts in the development process.
DSM raises the level of abstraction beyond normal programming languages by directly specifying the solution in a language that uses concepts and rules from the problem domain – a Domain-Specific Language (DSL).
It does summarize the problem:
There is increased awareness within the modeling arena of the need for
a central repository of system description information.
This is brought on by a growing recognition that only with a strong central repository can modeling tools be integrated, cope with large projects, provide full life-cycle support, produce complete documentation, perform system-wide validation and verification, and adequately control a project.