For most optimised HTTP/1.x sites there's already a complexity cost of merging JS files, merging CSS files building sprites - including the tradeoff of getting the bundles right, which of course reduces cachability.
If you are revving your bundles with hashes (main.8a4ce55.js), caching shouldn't be a problem. Not sure what your build process is, but there are plugins to do this on most setups.
When two separate resources together at build time they're being coupled from a caching point of view if one gets changed and the other doesn't they they both have to be re-downloaded because the bundle has changed.
And all of this is a build-time problem.
If we're going to engineer the HTTP-protocol to solve build-tooling and development related problems, we might as well add JS-linting and minifying to HTTP itself as well.
Seriously: This problem is best solved elsewhere.