In TFS 2010, we made integration of TFS with Sharepoint and SQL Reporting Services optional.  You can choose not to install them, you can choose not to create sites even if they are installed, etc.  As part of this, you can also configure your TFS server to point at centralized Sharepoint and reporting infrastructure, etc.  Basically, we've made it really flexible.

It's all well and good until you create your project, decide you don't need/want Sharepoint and then come back later and decide you made a mistake.  How do you get your Sharepoint and Reporting sites.  We knew this was going to be an issue, but unfortunately, we didn't have time to make it a seamless experince.  In the TFS 2010 RC release, we have, at least, made it possible (if difficult).  Once we get the product shipped, we plan to add a Power Tool capability that will make the experience nice rather than making you edit XML files.  Fortunately, it will be a relatively small minority of customers who will ever need to go down this path.

Gregg has written a post showing how you can do this on the RC today if you really need to: http://blogs.msdn.com/greggboer/archive/2010/02/24/creating-sharepoint-portals-reports-and-upgrading-reports-for-an-existing-team-project.aspx

Brian