I'm of the opinion that Peter is in his original universe, not another reality like he's been convincing himself. The only different is that without his presence, the timeline in this universe has run a little differently.
The Olivia, Walter, etc are all too similar to the earlier ones for me to accept it's a different reality entirely, and there have also been some subtle hints throughout the last few episodes that this is his own reality - he just doesn't know it yet.
We have to remember that Peter himself is not aware he was wiped from existence. He appeared in the lake, and as far as his perception is concerned, he's in a different universe because no-one recognised him.
Now people are starting to remember him and his timeline is starting to correct itself. In a way, his re-appearance in lake is symbolic of the timestream - the ripples from his re-introduction into his reality are starting to emanate out and be felt by others, manifesting itself in the restoration of thoughts, feelings and memories associated with Peter's original existence.
The big questions now are:
1) What caused his re-appearance? Was it the machine? Was his effect on Walter/Olivia/etc so strong that he was subconsciously willed back into existence by them? Or was it some other external force?
2) As people start to remember more and more, will this timeline be restored back to exactly what it was at the point of Peter's disappearance last season? Would this mean that people like David Robert Jones will effectively vanish, given that he died in Peter's original timeline?
3) If all this comes to pass ................. what has been the whole point of Peter's disappearance and reappearance, as far as story is concerned? We would simply be back where we were at the finale of last season. I think there's got to be some other purpose to all this.
