ASP.NET MVC and Mootools

ASP.NET MVC includes JQuery, which seems to have Microsoft endorsement. However, there really isn't as much overlap (as before) with the client-side Javascript framework and the server-side MVC architecture.

Using jQuery, MooTools, or any other such structure when delivering Views is really independent of MVC itself. You are probably more interested in how MooTools can integrate with ASP.NET AJAX, which I believe is considered an MVC component.

Here is this blog on ASP.NET AJAX and MooTools.

Please note that this MS is putting a lot of effort into adding Intellisense support for JQuery in VS2008. It is possible that a third party might make the same effort to support MooTools in intellisense, but then they might not be, something worth considering if you are not too attached to MooTools.