My question is always this: "What does Apple have to win by locking down OS X the way they locked down iOS?". Even a single good argument would surprise me. The only thing people can come up with is 'make more money by selling applications through the Apps store'. Meanwhile Apple barely breaks even on the iOS app store, while they make billions selling hardware and selling music (DRM free, by the way). Somehow it doesn't really make sense introducing reasons for people not to buy Apple hardware, such as restricting what they can install on it.
People made the same argument you're making about dumping Classic (i.e., dumping Classic effectively restricts what can be installed on a Mac OS X machine), but Apple did it anyway. They did it to force user base migration to the new technology (i.e., Mac OS X).
Apple wants to move most or all of its user base to a unified OS that is more like iOS than Mac OS X. We know this because of what Apple themselves have called "Back to the Mac," i.e., bringing features of iOS, such as full screen apps, a home screen like the iOS home screen with app buttons, and an App Store to the next version of Mac OS X (a.k.a. Lion).
Why do they want to do this?
Because over the past decade, Mac OS X product revenue has gone from 90+% of Apple's revenue to less than 30%, and Apple sees this trend continuing. Like it or not, iOS is now the dominant Apple platform, not Mac OS X, and Apple would like to move as many customers as possible to iOS. They'll transition them by making Mac OS X more like iOS, then they'll unify iOS and Mac OS X. Most customers will buy iPads or variations thereof; others will buy iBooks running iOS not Mac OS X; only a few dinosaurs and developers will continue to run Mac OS X.
The Mac App Store is not a plot to take over the Mac software market, though it will be a small profit center for Apple. The Mac App Store is part of a long term plan to accustom Mac OS X users to using iOS, because in the future, they will mostly be iOS users, not Mac OS X users.