Plus the dependencies. With app stores you (usually) get one program and that's it. It works. With package systems you have to install several dependencies for each, sometimes an absurd number (say, 100 packages to get Gnome). And then there's dependency problems (had my share in Debian at older times).
At the core, dependencies are a good thing, although there's downsides to that as well.
I have no experience with desktop app stores, but you wouldn't get Gnome and similar large and complex software from one, would you?
Which makes your comparison pretty unfair.
