I am leading a pilot currently of the new development platform, Team System, at work. We are currently only running the pilot with a single small team. It's too early to tell yet how succesul this pilot will be or what the overall challenges we'll encounter, however, so far I think the biggest item that seems to be a struggle is education.
When I say "education", I mean in terms of understand the process and concepts behind what Team System gives us in the way of value of reporting via deep metrics as well as an integrated tool set. The current state here, as I assume at many small to mid level .NET shops is that we use Vault for source control management and FogBugz for work item tracking. Just by consolidating those activities into a single tool (for the developer, it's just Visual Studio, to manage coding, unit testing, source control tasks, and work item management) saves time and effort. We are still in requirements gathering and design phase so those features have yet to be fully realized, so I am keeping my fingers crossed.
In reading my feeds this afternoon, I noticed Rob Caron had just posted a gem that provides links to case studies of how other companies have made the migration and the results they are seeing.