"So Bruce grew up with only Alfred, the family servant, for companionship...."
2. Rodney at the firing range. Rodney and Elizabeth? (and Radek? or a whole bushel of civilians?) Because John's seen enough of the future to know that the Marines aren't going to be enough to keep everyone safe, so the rest of the expedition needs to be able to defend themselves effectively. (Also, Rodney at the firing range seems like comedy gold)
3. Ford learns to fly! AKA Crazy John's flight school.
4. Sanctuary remix: in which John spins things a little to Sumner, Chaya is less than helpful, and the audience gets something like an explanation for the way things happened the first time around.
5. "Once upon a time," he said, and closed his eyes so he could pretend no one was listening. "Once upon a time, there was a boy named John."