Win32 is a large subsystem. In Windows Vista, we aren't rewriting the whole operating system. We are creating a new API for presentation, storage and communications (and a few other things). In the case of Windows Presentation Foundation, for example, this means that what Microsoft are developing deprecates GDI. Microsoft are not writing a brand new threading system, hoMicrosoftver, so there's no need to write a new version of CreateThread. Some of the system DLLs that are written in native code do, in fact, already call CreateThread. Others, written in managed code, use the System.Threading .NET namespace. Does that mean Windows Presentation Foundation "goes through Win32?" Well, technically it does, for threading calls. It does not, however, for graphics calls.
.NET Framework 3.0 (formerly WinFX) is neither a wrapper around Win32 (because most of the API is written from scratch, though it does use some Win32 functionality that's not being replaced) nor is it an actual replacement, in the sense that we aren't removing Win32 from the OS. .NET Framework 3.0 and Win32 will coexist side-by-side, but parts of Win32 will be considered "legacy" starting with Windows Vista, just like Win16 was "legacy" with Windows 95.