The MAS is in a strange place of having to push out some stuff (e.g. Xcode) that is entitled to mess around with your system, for necessary reasons (e.g. to install a debugger.)

There only a few ways they could have worked around this, and I don't blame them for their choice:

• Require apps to sandbox themselves to the degree they're able, and then request "entitlements" for anything they need to do outside of the sandbox. Use entitlement list on app submission to guide the app review process.

This is what Apple chose; it's not very costly for them, since they were already doing review on app submission, and the entitlement list can actually make review faster than before, since it gives each review-iteration more of a clear picture of the app's architecture.

• Divide apps into "system" vs. "pure-userland" apps. Run all "pure-userland" apps in containers. Optionally, require that "system" apps are as minimal as possible—more like "system extensions"—and set it up so that most "system apps" end up as "system extension" + "pure-userland app" pairs that use IPC to coordinate, where one has some sort of official UX to trigger the app store to download+install the other. Require, additionally, that the "pure-userland app" still retains some sort of usefulness even without the system-extension.

This is a cool solution, and the one I'd expect Linux (or Android) to use in the future, pairing "app" packages with "system" packages. It can be nearly completely automated with little-to-no review required. But it is very restrictive: either you're containerized or you're not. The components that require elevation can't benefit from isolation at all. There's no partial sandbox in the sense of Chrome's "even if you get write-memory access to the browser, you're not getting anywhere" sandbox.

• Do what iOS does: have only pure-userland "apps", but where some apps can prompt you to install configuration profiles, that then apply a layer of (reversible-by-uninstalling) changes to the OS, which the app can rely on. This is how e.g. the MaaS360 app "takes over" and manages corporate iOS devices.

I could see OSX being written this way. OSX has configuration profiles(!), though they're not used for nearly anything other than enterprise management (and, I think, the recent-ish OSX beta program.) Personally, I think they're a cool system, a bit like if the Windows Registry was composed in terms of immutable, introspectible patch-layers rather than being a single mutable tree. (By analogy: applying a configuration profile is like applying a filter in Flash or Fireworks, while installing a .reg file is like applying a filter in Photoshop.)

The flaw with configuration profiles is that you have to anticipate every way an app might want to modify the system, and provide an API to request that the system modify itself in that manner instead. You might be able to anticipate e.g. MacFUSE's desire to install filesystem drivers, or f.lux's desire to play with screen gamma, or even Synergy's desire to take over your input device handling. But you'll inevitably miss things, like e.g. Dropbox's desire to inject a shared object into the Finder that overrides some of its exported functions with new ones.