> The problem is, programs need to be able to access the system
Not necessarily: to be on the Mac App Store, an application must access only files in its own resources (configuration and so on) or through user interaction (open file dialog). If your web browser gets infected, it gets full read access on every file you willfully want it to read. Problem, you cannot have a multimedia player that opens m3u playlist files in this model: see http://mplayerx.org/leave-mas.html
Not necessarily: to be on the Mac App Store, an application must access only files in its own resources (configuration and so on) or through user interaction (open file dialog). If your web browser gets infected, it gets full read access on every file you willfully want it to read. Problem, you cannot have a multimedia player that opens m3u playlist files in this model: see http://mplayerx.org/leave-mas.html