I would like to see ClickOnce applications install through the App store...

Also the current model seems to create problems for people who want both Immersive and Desktop versions of their apps, where the two versions would switch between each other. You would have to tell the user to download two separate apps in two separate places, leading to a complicated install process. I think the "full screen mode" metaphor that Apple is using is basically a good idea, and all of these steps in the middle would break that type of metaphor.