"We are not allowed to distribute updates through other channels to apps which were purchased from the App Store." The solution is simple. All Mac developers should stop selling through the App Store, regain control of the distribution channel, and leave the Mac App Store barren of quality applications. Until Mac developers have leverage, Apple will continue taking their 30% cut and enforcing rules which suit them an…
You don't have to wait for Mavericks, it has already happened. Apps that are sold through the App Store can not make use of the the media keys on Apple keyboards, which is why VLC can use them and other apps can't. Edit: other than iTunes
The App Store may offer things like the iCloud SDK but will restrict apps from using features that compete with Apples own apps, as well as any cool hacks which apps outside the App Store are free to make use of.
My take is that Apple is herding developers into the App Store, enticing them with SDK features and the promise of riches, and at some point they will change the default gatekeeper setting so that users see great big warning signs and are too scared of running non App Store software.
We're probably still a few years away from this happening, but the writing is on the wall.