I don't think that walled garden is technically applicable to the wild of the internet. Apple dictates (negotiates) the terms with the iOS carriers and can ensure that direct connections between iOS devices over the carriers is possible for the apps Apple wishes to whitelist.
Facetime over cellular wasn't enabled as a feature until last year, which means during the time period discussed in the patent lawsuit (last year) it was either non-existent or very new with minimal usage. Some carriers still don't allow it at all. For the most part it is/was a WiFi application meaning Apple has no special relationship. I'm pretty sure other applications will show similar statistics.
"Direct connections" can also be deceiving. This could include direct connections from one client to another, where that other client is acting as a P2P relay. Skype used this, because not all clients could punch a hole across NAT. So then you had some clients who are not reciprocating so that is the Tor model where some clients are relays and others are not.