The core is definitely working through the issues that arise trying to support the MS AJAX framework. Here is a summary of what I know (and don't know) thus far.
1) ScriptManager (the component that makes all the MSAJAX functionality work) requires Full Trust to work in the bin folder. You can get it to work in Partial Trust if you install it into the GAC. Due to this issue it is going to be nearly impossible for DNN to completely integrate it into the core. Any solution that is done will more than likely need to be Optional.
2) Even if we did make it not-optional, I do not think we could distribute the dll into our zip. I may be wrong here, I am not good with legal stuff... If this is true, then the DNN install would not simply work out of the "box". I realize that some people will draw the analogy that this is just like needing the .NET framework and IIS... Personally, I don't feel that these are the same thing though.
3) I envision the core going the optional route. This would be done by reflection, similar to our provider pattern. I envision the core "registering" the ScriptManager on the page in a similar way that a developer registers a ClientAPI script. The reason Vladan offers a separate dll httpmodule is he did not want to modify the core, this is a good approach, unless you can officially modify the core. Hopefully this concept gives developers an idea on how it can be optionally included.
4) There is a major misunderstanding about MSAJAX that I am seeing. People are confusing MS AJAX with the Control toolkit. MS AJAX only has two or three controls included (UpdatePanel being the primary one). The control toolkit is a community project, with its own release schedule. If you think about it, you probably will see a lot of similarities to what I have created. We have the ClientAPI, which is part of the DNN Framework. MS has MS AJAX that will soon be a part of the .NET Framework. We have the DNN WebControls, that utilize the ClientAPI framework to provide advanced GUI experiences. MS has the Control Toolkit, that utilizes MS AJAX to provide nice experiences as well. Right now, DNN ships both the AJAX Framework (ClientAPI) and the webcontrols with each release. This eases the burdon of the module developers quite a bit. Not only do we guarantee compatibility between releases but we also get to distribute it. The case for MS AJAX and the control toolkit will not be so easy. Some features will be integrated into the core like version checks for modules, but it is going to be a bumpy road at best (IMO).
I'm spending too much time on this post... there is still much to discuss... just need to find the time... hopefully this info sheds a little light on the subject.