@wastingtimewithforums: Well, for one thing, the App Store is a Metro app and can't run Desktop code (like Win32 installers...). Secondly, the app store is for Metro style apps.
Desktop application installation is a complex beast and you can't simply remove the complexity by packaging a la appx. It's a completely different model.
As to other reasons that aren't as obvious as the ones I listed, you'll need to ask the Windows Store people.
And Microsoft has some of the bits right now to create a non-metro app store .... take the .Net "Click Once" tech and tweak it a bit and you could have managed desktop app and XNA games published and sold and updated via an app store system.
yes that would still leave Win32 apps out of the picture but I can well imagine that a huge number of dot net developers would find this interesting if MS did it.
there is only one reason Microsoft is not doing it, they do not want to.