Would it be bad though? A lot of APIs change in the browser space. WebRTC was broken a hundred times. Libraries depending on Prototype would probably be old, maybe insecure. You need to break it from time to time, you can't be backwards compatible all the time.
Would it break the web though? Wouldn't they just override the native implementation with a JS one?
Then the two implementations would probably be incompatible (different signatures, different implementation / return values) and would cause unexpected errors down the chain. So, essentially, breaking the web and making it difficult to fix it.