I'm not asking this to fight - I genuinely don't know :/
What does the government have to do with what software is going to make it onto a tablet?
Isn't that like blaming the government because Samsung didn't put USB3 on their new TVs or DLNA or some models?
No worries, I'm sure I understand the question.
Basically Apple has always enforced full control over its platforms -- and with iOS it was no different.
Without arguing the pros and cons; the primary reason Apple takes this approach is to ultimately guarantee the end user experience.
In the iOS develop circles, the only official way to develop apps was to use either Xcode /Objective-c or HTML5 with iOS multitouch extensions.
Then as with any popular platform, other multi-platform development environments started being adapted to create apps for that platform; in the iOS case, the following were the primary ones to emerge:
1. Unity (c# based OpenGL game development studio)
2. MonoTouch (c# based .NET port for iOS's unix environment)
3. Adobe Air (ActionScript)
Ok let me try to simplify the key difference between these:
Unity and MonoTouch compiled to native Arm processor code and by in large are indistinguishable from an App compile with Apple's dev tools -- similarly they run equally fast.
Monotouch in particular maps 1 to 1 to the full iOS SDK.
Unity is OpenGL focused so the need to map to the iOS SDK is not necessary as the compliance standard is OpenGL.
Adobe Air is different; basically they wrote the equivalent of the Air client (flash type client) as an App and then the ActionScript is packaged at "compile" time into something that resembles an iOS app. There is no direct relationship between ActionScript and the iOS SDK and also none with OpenGL. The reason they do this is to only support common functionality between the multiple platforms they support. For example if the iOS sdk does not support a feature in the Android SDK, the it is not supported. Implementation of functionality is imbedded into the app engine (similar to the flash client on desktop pcs)
Mono approach is always to support all features on the targeted platform I.e. 1 to 1 SDK compatibility, so too for Unity in respect of OpenGL.
Adobe try to shield their customers from the underlying complexity of each platforms' SDK and OpenGL -- but this of course comes at a price:
1. Apps are slower.
2. Apps navigation is typically strange and inconsistent.
3. UI look and feel is alien on each targeted platform (iOS, Android, ...)
4. The stability of the apps are solely dependent on the Air App engine -- sadly Adobe has not been known to produce very robust, fast or stable engines.
5. Many of the hardware differences are not supported, for example: initially the gyroscope was not supported, and similarly the barometer, compass, ... Well not until most platforms had support for this.
Ok back to the Gov bit:
Apple wanted to prevent this type of inferior apps on its devices, so it changed its developer terms to strictly prohibit anything but native compiled arm code , for example: Xcode / objective-c (the primary target being Adobe)
Key many Adobe public adverts re being shackled by the new Apple terms, and finally you have the Gov's attention.
Instead of challenging this legally Apple chose to adjust the development terms to permit all development environments.
So in the end we have good Apps that are produced by in large by Xcode / objective -c, Apps produced by Monotouch and Unity that because of their design (mapping to iOS SDK and OpenGL) and native Arm compilation perform in most cases just as good as the Apple dev ones and look and feel just like the real thing.
Then unfortunately we have apps created by Adobe's Air mess... very evident in the Magazine space. You won't find any best seller Apps made with Adobe's tools on either iOS or Android.
Complex question, hopefully the long description makes it easier to understand why much of this magazine mess is beyond Apple's control.
Think for example the fact that Adobe tools do not map to Apple's iOS SDK -- so simple things like background downloading are completely dependent on Adobe implementation in Air / Flex -- and improvements are solely dependent on when Adobe decide to fix them or include functionality for it.