Skin graft idea was just bad and seems more implausible than heart surgery.
I thought they might be heading to the "John's son is the real saviour of humanity" angle. But they didn't.
Also, wasn't the mute little girl really God? Because that's what I read into it.
In terms of Skynet always winning vs. Connor's destiny. It seems Skynet's contingencies are matched by equal attempts by the Resistance to stop Skynet before it's even created.