Okay, only problem I have with Hanso having faked the crash is that in flashbacks, we see the others watch the plane break apart. That would mean that Hanso not only brainwashed the survivors of 815, but all the people already on the island as well.
Here's a question - how in the heck did John's father get to the island? Sounds like he was kidnapped and brought there vs. some mystery teleportation explanation, but if the others no longer have any communication with the outside world and the beacon is out and the sub is gone - how did they manage this? Or did they bring John's dad before all of that happened?
Question #2: Why in the heck does John need to kill his dad to please the island? I thought for sure that when he refused to kill, the others would say that he PASSED the test of not being corrupted or evil. Whoever's running things has some very odd ideas about ethics.