I had picked up a couple spoilers from the 'net snce the finale aired, so I wasn't completely shocked by Nimoy or the whole AU thing. In fact, the execution was actually a bit better than I expected. The part that gave me goosebumps was Walter going to Peter's grave, even though I knew about that part too and had been picking up on the little clues... his not remembering these childhood events, and in 'Inner Child' when he remembers the scar on the action figure being on the opposite side, and Walter's repeated mentions of Peter's childhood illness. I think generally Peter was underused this season -- he was Walter's guardian, the frustrated son, the connection to shady types, the guy who owes money to Big Eddie, but he was still very much in the background. I hope this revelation means that we're going to see more of him next season.
There's definitely some parallels to Alias here, most notably children being trained and tested at a young age for something dark and mysterious. Cortexiphan is something that, when administered to a young enough person who is then 'activated' through tests such as the light box, awakens certain potentialities. For the twins in 'The Road Not Taken', it was pyrokinesis... with Nick Lane in 'Bad Dreams' it's some kind of empathy. I would guess that Olivia's ability has something to do with being able to jump realities, but then there's the old video Walter had of little 'Olive' sitting in a room that looked like it had been set on fire.
Two more things -- the near accident Olivia had on her way to the hotel obviously is meaningful. So is the fact that when Peter finds a dusty picture of his family, we never see a clear picture of his mother. IIRC, we don't even know if she's still alive... but I'm betting that she is, and that she's someone important.
Oh, and one of the best lines of the series; I laughed and scared the cats:
"What are you doing here?"
"We're trying to plug a hole in the universe. What are you doing here?"