Do you have a proposal to achieve solving it at the version control level that doesn't require either a complete paradigm shift in programming and data formatting langauges to everything being trivially an AST or embedding knowledge of every format ever invented to your version control?
Because it seems a lot easier to just design newer languages to be friendlier to version control than either of those. JSON has little excuse here, even when it was 'invented' it was a bad idea to simply run it through eval and pray it had nothing malicious or damaging in it, so compatibility with IE6's stupid parser wasn't really all that special. Never mind that it didn't take off as a really popular format until well after that was a concern.
If you store JSON in a version control system, then it is usually hand-edited JSON. (If it is generated programmatically at runtime, then the data is in a database.)
And if a file is hand-edited, it's format should have niceties that make hand-editing more pleasant, like optional trailing commas, and comments.
By making the format more suited to hand-editing, you also make it better for diffing and VCS.
