As I understand it, the main objection to `__proto__` is that it's writable, and thus not atomic with object creation. This creates a bunch of headaches for implementors for performance and security.
More knowledgable people than myself discuss it on this es-discuss thread: http://www.mail-archive.com/es-discuss@mozilla.org/msg06142....
There is a Harmony proposal for a "set prototype of operator" that would solve this problem; instead of writing:
var newObj = {__proto__: OldObject, id: 5}
var newObj = OldObject <| { id: 5 }