What if you want to restore your computer from Time Machine? Normally you would boot from the OS install disk, plug in your Time Machine disk, and it would restore your computer exactly the way it was at a given point. How would you do that with an App Store download, since you can't boot from it, thus you can't erase your system and restore it should you need to?
I'm sure apple will add some type of utility into time machine for those who don't have a disc to boot from... don't worry they aren't going to abandon time machine because of the mac app store.