Lots of websites still use Prototype.js. Magento still has it as a dependency. Don't want to break the web!
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.
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.