In theory, supporting backwards-incompatible changes should be well possible with versioning (with, e.g. the <script>'s type attribute or a <meta> tag, or "use jquery14"; magic string or whatever) - everything should work as long as one can specify "I want libfoo API v2 here".

Right, that is the advantage of having an API layer that the developer (not the web platform) controls. The more we dump into the web platform the bigger it gets because it's nearly impossible to remove anything. The idea of the Extensible Web Manifesto is to provide primitives in the web platform and let people build more powerful abstractions over them in JavaScript.

You could view jQuery as that type of abstraction. If you decide to use some other abstraction (e.g. React) you can switch your web page/app and you aren't paying the cost of having jQuery embedded into the web platform.