The trouble is that apps don't run isolated from the OS. This makes things easier (as this is how stuff works on desktops, too) and more efficient (no middleware overheads), but at the same time exposes the OS to more unpredictable situations (bad packages will always be a problem), and the fact that the users get root is not helping in this regard either. As long as we don't have at least a chroot separated environment for apps, stability will always suffer.