Well, for most large organizations or Professional Services Firms, methodologies around developing software are pretty important. Perhaps more important is the fact that upon picking a methodology, if successfully implemented, and organization can gain significant savings in the development lifecycle. (Some organizations, sadly, get into process paralysis, which actually causes the opposite effect, but that is beyond the scope of this post!)
If you are part of an organization that has a successful process, you probably want to continue to use it. And if you've really taken a look at Team System, you are probably as excited as I am about how the entire development lifecycle can be greatly eased through the use of the built in tools. From WorkItem tracking, reporting, Source Control and Project Management integration, the list goes on and on.
You might also be concerned about the fact that in Beta 2, the only Methedology template we shipped is MSF Agile. Since most organizations do not use MSF agile, this means the process, out of the box, is probably not going to match up with your methodology.
Good news and Bad news for you. First, the bad news. There is (as of now) no single tool that will allow you to build out your own Methodology for VSTS in a wizard-type process. The good news is, of course, you can indeed extend, change, expand, and remove parts of the default template, or indeed create your own. The Visual Studio 2005 Team System Extensibility Kit Beta 2 is what you are looking for to do this. It explains every part of Team System extensibility, and presentation decks, samples, and drilldowns on all of it.