We don't know what will be blocked by this, but as I stated before. Tools that aid development for the iPhone platform will likely go untouched. Many expect Unity3d will be fine.
Things that try to be wedge another platform on top, like Flash, will almost certainly be banned. For solid reasons.
You do understand that Unity is not iPhone exclusive right and that it doesn't let you write your apps in C, C++ or Objective-C ? So apps are not originally written in the languages approved by 3.3.1.
Unity is a wedge on top of the iPhone, just like Flash would be. The user needs to know Unity, not Cocoa to do work with it.
And again, there's nothing wrong with that, and until further evidence in a released product, there's nothing wrong with Adobe's approach either (do you have early access and could provide insight into the flaws of Adobe's packager ?).
In the end, it's all ARM machine code. The tool does not affect the quality.
That's exactly it. It's a numbers game. If 85% of Obj C apps are garbage according to somebody's metric, betting odds are that that number would go way up over 90% for Flash-to-App ones using that same quality metric, whatever it is.
No. This gives fault to the tool rather than the developers. ActionScript is a programming language and Flash/Flex are tools that use this language in order to provide programmers with a way to output ressources. By definition, it is the same thing as Interface Builder and Objective-C.
There is no fundamental difference if Adobe built a way to compile Actionscript into ARM machine code. In the end, it's all machine instructions getting executed to load files and output them through proper channels (audio, display) and to process input.
To try to give a tool a bigger role than that is quite simply either very ignorant of programming or just fundamentally paranoid and irrational.