First of all, no, Prototype isn’t completely gone, yet. I know I didn’t expect it either 😀
And here comes my question: why? What happened with Prototype?
Well my theory is simple: Prototype is just too complex.
On theory, sure, it sounds cool – you have objects on the back-end you have objects on the JS front-end, you can reuse functionality and structure logic and etc.
On practice though is more redundancy than good design concept (in my opinion), because you need to program (more or less) the same models twice.
If Prototype was more like ClojureScript and gave you possibility to transfer automatically the domain objects to JS front-end object I would actually understand the point of having Prototype but as it is right now in my opinion – having objects just to gather properties and functionality is not good enough reason to have them.
Btw if you haven’t check out ClojureScript before please do, it is awesome (on a concept level at least :D)