One of the requirements of all apps in the Mac App Store is that they “play in their own sandbox,” meaning that, like iPhone/iPad apps, they can’t interact with other applications or the larger operating system outside themselves.
While this might be fine for many games and productivity applications, it is certainly going to be limiting to power users, developers, and longstanding Mac customers who are accustomed to being able to get software that can potentially make the computer do, well, anything. As is consistent with Apple’s direction over the past many years, this will indeed increase security and dependability for the many, while decreasing power and flexibility for the few.
If sandboxing at all concerns you, you may wish to check to see if a developer offers a directly-distributed version (that is, not through the Mac App Store) which doesn’t have these limitations. On the other hand, if security is of primary importance to you, you can feel safer sticking with the titles Apple has authorized the distribution of through the Mac App Store.