The issue here is that everyone ASSUMES that the Mac App Store will become a hit, no matter what Apple does with it. They also assume that the Mac App Store will absolutely become the ONLY way to get software on a Mac eventually. I disagree. I think Apple will have to approach this store a bit differently than the iOS store if it wants to get enough developers in to make the store worthwhile. And while I think Apple would love for the Mac App Store to be the only game in town, that’s by no means going to happen if Apple blocks some of the most useful software available on the Mac today.
At the same time, many developers are going to be forced to move towards Cocoa, forced to stop using crappy installers that put files all over the place, forced to adhere to interface guidelines, forced to stop using copy protection that hurts innocent buyers—this is all a good thing. They will also be getting a huge influx of competition from iOS developers who turn their sights towards the Mac. Evolve or die. And that’s great for the users.
Ultimately, I think there’s a very decent chance that there will be movement on both sides, with Apple loosening up the guidelines over time, and developers tightening up their bad coding habits and being forced to find more innovative ways to accomplish what they want to accomplish.
And Apple will get what it really wants, which is to kill Java, Flash, Carbon—all the old legacy dead weight holding it back from moving OS X forward even faster. Jobs wants control, like he always does. You can disagree with whether or not that’s a good thing, but time will tell if it leads to better things.