I work in academia, and can say that software updates via the app store is a royal pain in the ass. Really creates headaches for our lab managers when they need to update the software in OS X 10.7.
Since Lion, I went from loving Macintosh for the last 6-7 years, to now thinking about switching back to Windows. This crap about making the desktop OS work and feel like iOS feels like a huge step backwards. I am also very turned off by the whole App Store integration. Maybe this works good for home users, but for users in corporate and academia, it creates all new headaches.
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Worse than that. Since you don't want the App Store on end users machines, and public machines, you need to download the updates to a main computer. Then push them out by hitting all of the machines manually. Really obnoxious.
Thats' crazy.