> Unofficial clients for websites such as YouTube that add features that official client doesn't have.
I'm sure Google can send a cease-and-desist to all sorts of other stores instead of just Apple.
> Tools to disable advertisements in applications.
This would be breaking the sandbox model of the system, I don't think the regulation requires dismantling system security
> Programs licensed under GPL as Apple App Store bans those.
No such rule. VLC on App Store is the first example that comes to mind. There are also GPLv2 components (such as WebKit) shipping in iOS itself.
The FSF has said there are (IMHO bureaucratic) issues with GPL on an App Store, specifically that e.g. Apple takes on certain responsibilities, rather than the developer.
For that reason, it's possible a contributor may shoot down publication, which IIRC caused VLC to have to rewrite certain components before launch.