I do have a tendancy to get annoyed when I think about Microsoft’s web offerings of ASP.NET and more recently their AJAX libraries. I’ve had a little rant about it before but I thought Adam Kahtava has written a good post on the AJAX side of things here, The ASP.NET AJAX Framework is for DUMMIES!
I’m not sure I’d go so far as to say the library itself is bad, IMO it has a lot in common with Prototype, but I certainly feel the pain of pandering after the server controls. Although there are a number of "pure" AJAX libraries to choose from some also have projects/extensions to help with server controls, e.g. http://www.codeplex.com/YuiDotNet, so maybe you can move to another library without leaving the server controls behind.