Pros and cons of MS Ajax vs. jQuery in an ASP.NET MVC app?

Personally, I would stick with JQuery. MS AJAX is pretty heavyweight in terms of size and you can do so much with JQuery. As far as whether it is easy to convert code, well it depends on how much of the MS AJAX stuff you are using. I don't think there is really much appreciable difference in debugging from one to the other. You will have a larger community of JQuery users from which to pull resources.

You can (and I do) use both depending on the need. When I want a particular form to be non-javascript friendly AND I'm generating content on the server, I'll use MS AJAX via the AjaxHelper. It builds everything I need on the client side to handle the non-javascript enabled browser. I only need to detect AJAX/non-AJAX in the controller and return a partial or a full view depending. If I need to use AJAX as part of a plugin (say autocomplete), then I'll use jQuery. The point is I use the tool that best suited (easiest to implement) for me. Granted, most of my apps run on an intranet so I'm much less concerned about the size of the downloads.

I also found the jQuery announcement about MS incorporating the library

Apparently :

Additionally Microsoft will be developing additional controls, or widgets, to run on top of jQuery that will be easily deployable within your .NET applications. jQuery helpers will also be included in the server-side portion of .NET development (in addition to the existing helpers) providing complementary functions to existing ASP.NET AJAX capabilities.

So I'm thinking its quite probable that they'll end up having jQuery helpers that exactly mirror the AJAX helpers for the MS stuff.

I guess solution I'll take is to use Html.BeginForm, and then intercept the submit button to use jQuery. I'm not especially worried about people without javascript losing functionality, but its not that much harder to do so I may as well.