The big difference being that the App Store will be preinstalled, and probably have a default place on the Dock and a permanent home under the Apple menu in the top left of the screen.
I'm hoping, but not expecting, that the App Store will replace Software Update, so updates to Safari/iTunes/etc can show up right next to updates to your own installed apps, and OS security updates can just be treated as updates to the (non-removable) OS "app."
If you want to keep getting updates to Safari, etc., you better have the Mac App Store installed which will (coincidentally) try to get you to spend cash money while you're in there.
