,AndyC wrote

*snip*

They'll have the desktop, but people probably won't want to use it. It's a very clear statement that, going forward, plugins are being deprecated in IE. Creating content that doesn't require plugins is ultimately better for the web and applications too complex to be easily developed in HTML are probably better off as native WinRT apps anyway.

With the Windows App Store, Microsoft has the same motivation as Apple does to deprecate plugins in Metro IE.