One of the key tenets WiX development is operating under is to make all changes available to both community WiX as well as "Rosario" WiX. (They actually get fixed for the community first :))
Each time we make a major "Rosario" WiX release, I plan to list the major differences between community WiX and "Rosario" WiX.
Signing - The WiX binaries shipped with Visual Studio will be signed with a Microsoft signature rather than the community WiX signature.
Contents of the installer - In order to limit our test surface and ship the mainline tools in the highest possible quality, there are a few tools that will not be shipping in the VS package. Another option we are exploring is to supply some sort of SDK for the tools we don't plan to provide mainline support for.
Supported VS versions - The "Rosario" WiX toolset will only install on VS 2008 while the community version will continue to install on both VS 2005 and VS 2008.
Nant - No support for Nant will ship in the "Rosario" box.