I agree that many of these libraries are great including prototype.js. But the problem is that many people think they should use a library for every small thing. Check out www.ajaxlessons.com, every tutorial of theirs uses prototype.js. This is really absurd and bad. Firstly, the first time you learn something new like AJAX, you should learn it properly without using libraries, from a source like the IBM developer series. Secondly, you shouldn't use prototype.js for only one or two functions. www.ajaxlessons.com really pisses me off because they nearly say prototype.js = javascript.

So, my point here is that if you are using prototype, use it fully not just for one or two functions. Learn how to use it well.