Also, there are apps that you use more often and apps that you use less often. By leaving the update to the app itself, you can basically make use of the update mechanism in proportion to how much you really need the app (you start it up, there is an update, you run it in 10-15s and you're done). You haven't used it in half a year, you open it, update to the most recent version, done.

With the appstore on the other hand, besides being horribly slow, it will always present you everything that is updateable, even if you only need that tool only 3-4 times a year. So I will always have to make that call per every app in the list, every time I open the updates panel.