Modern additions to ASP.NET like Control Adapters and Atlas/AJAX muddy the waters even more and make it harder to have a "clean" project.
I also miss VS2003's Web Application project model (VS2005 SP1's still doesn't support WebDAV). VS2003 was also faster at Remote Debugging.
I often wished my biggest issue with maintaining a project not I had nothing to do with was tool choice. Often it is working with hacked up solutions and debungling poor practices based on design as you go planning:). Which is a chronic problem with small teams it seems lack of formal planning with architecture. I know that may sound like a good thing but it is like lacking DNA during prebirth. How do you build an arm that talks to the shoulder if you can't agree on design?
Not sure about either of techs you mention. I use Telerik professionally, so I never had to work directly with AJAX or specifically microsofts implementation. Telerik's implementation is good as long as you don't have to AJAX accross User control lines. They are working on that for the next release with AJAX Manager Proxy, which only becomes the manager when one doesn't exist in its parents otherwise it bubbles up events to the parent manager. So if you have a search box and you want your Ad Rotator to know when someone hits search but the search box is a user control or if you want to pass the search input to another control via some event (OnSearch).
Schedule is usually more prohibiting than money, so we pay someone else to figure it out like Telerik