Asp.Net AJAX was designed for Asp.Net WebForms, not MVC. It was designed to do many things that jQuery already did. Before MS agreed that bundling jQuery with Asp.Net MVC was a good idea, Asp.Net AJAX was all they had.
Asp.Net AJAX tries to replicate part of the server side environment in the client's browser - you can see this with the MS-like JS namespaces. It was designed for WebForms when everything was based on the post-back model.
The MVC paradigm tries to decouple and simplify aspects of web development by being honest with how HTTP works. Asp.Net AJAX does not really fit in this space because of how tightly it was designed with WebForms. In the same way that you can hack get WebForms controls to work in MVC (because it's still built on the ASP.NET core) you can also get Asp.Net AJAX to work in MVC - but the real point is this:
jQuery and MVC (by design and definition) were meant for each other.
(hope my answer is not too subjective :D)