My understanding is that the patent nonsense forced Apple to transform FaceTime from a peer-to-peer protocol into one that transmitted all data through centralized servers, specifically Apple's servers.
That meant that if the goal was for interoperability, Apple had to either provide server capacity for a bunch of other people's traffic, or they would have had to come up with a way to federate the system.
Federation certainly could have been done, but that's a lot of sudden extra growth in scope compared to just taking what they had and releasing it.