Hello Jonathon Stevens,
The process of synchronizing area and iteration trees continuously is ideal for many and was certainly something we discussed at length when implementing our TFS integration solution. Unfortunately when dealing with TFS it is very difficult to know when an iteration or area has been renamed or moved (versus simply deleted), which presents many problems for synchronization. Furthermore, TeamPulse provides the ability to synchronize multiple TeamPulse projects with one TFS project via the use of different synchronization queries. These scenarios are common in larger enterprises (including Telerik internally) and are generally segregated by area and/or iteration. In these scenarios a continuous and full sync of areas and iterations apart from work items is not desirable at all.
In regards to initial project area templates this is a good idea and something I will add to our backlog. With our next release we have implemented some functionality designed to enhance project creation, however area setup is not currently part of our designs. This may be something we can do to further enhance this new functionality down the line. I have applied some Telerik points to your account as a form of thanks.
the Telerik team