@DeathByVisualStudio: Problem with that theory is that if you support it today, you're going to find your have to support it forever. Not only that, but making the exception for one plug-in opens the door to absolutely every other plug-in too. Metro mode IE is effectively drawing a line in the sand and saying no more, it's what many of Window's critics have been saying ought to be done for years.
Meanwhile, for those who do still need access, the desktop version provides plug-in compatibility and more importantly provides the environment any plug-in is expecting. Remember that there are plug-ins out there which are used for things like uploading multiple files that expect the user to be able to drag/drop files into the plug-in and that or similar are going to be scenarios that would never work with Metro IE anyway.