Bill Gibson has written a series of TechNotes that cover the concept of the System (and the System Designer) and its purpose. While I highly recommend you read all his TechNotes, these I feel are particularly insightful if you are keeping an eye on what is going on in the world of architecture tools. Link: http://msdn.microsoft.com/vstudio/teamsystem/reference/technotes/default.aspx#Architecture
Currently, many people regard the Application Designer as the core design surface. For VS2005, there is legitimate reason for this given that it offers the most value (as we cut back on features in the System designer). Going forward, we in the product group, really regard the System designer as the core tool targeted for software architects, i.e. the tool where we expect architects to spend most of their time.
Furthermore, there are some of us that really think of the AD as something that is useful for the enterprise developer. After all, I find it hard to think that the visualization of the applications in a solution is something that's use is limited to the architect. There has, additionally, been some hallway conversation on how useful continuous synch is to the architect; especially in light of "What if" design scenarios.