Just an update on my progress.
I was able to get AjaxUploader to work completely with the MVC3 RC2 Razor ViewEngine. The only really specific issue I had with regards to MVC3 Razor was as mentioned above. Although they did introduce a breaking change by introducing "ViewBag" as an replacement for ViewModel (in controllers) and View.xxx (in views), which is not really an AjaxUploader issure, but does break the samples if you forget about it.
Otherwise it runs smoothly modifying the sample3 sample for using Ajax. I do all my processing using Ajax from my controller returning a JsonResult as noted in the sample. Just have not found a way to completely get rid of the UploadHandler.ashx file yet. Would like to do so.