On the technical specs page for the new iPhone 6 and 6 Plus under the Video Calling feature you can see that "FaceTime over cellular uses H.264/H.265". As the camcorder function does not use H.265, I am guessing that Facetime is running the H.265 codec in software on the ARM CPU and possibly accelerated with the GPU. The previous iPhone also used a software based H.264 codec, even though the A7 chip included a 3rd party hardware H.264 encoder IP core. In my opinion this was because the 3rd party hardware H.264 encoder IP core was not capable of delivering the experience Apple required for Facetime (Latency, bit rate, error robustness, etc). I expect next years 'iPhone 6S' will include 4K and HW H.265.
It is also puzzling why H.265 is only supported when Facetime is running over cellular and not WiFi. This could be just an omission on the specs. If anybody has any ideas why this could be the case please provide a comment below.