iCloud document storage and Notification Center. Both of these are slated only for third-party apps from the Mac App Store. Many developers, though, have been maintaining non-Mac App Store versions of their apps. If this continues, such apps are going to lose feature parity between the App Store and non-App Store versions.
This will affect software from companies such as Adobe where custom installers are necessary and/or the economics of taking a 30% App Store hit is not necessary when they can already reach their customer base. The move strikes me as anti competitive.