Peter's appearance in the yellow universe may be a sign of things to come. As we know, Peter is something of an anomaly. Hence, the time distortion toward the end of the episode may be a signal that Peter's time here will be very limited, and Walter will have to overcome his angst from the reappearance of his son.
The translucent shapeshifters, like their predecessors, are part of a war between the worlds. Who sent these soldiers, and who will send the ones to come?
Yellow Universe General Differences:
Nina Sharp adopted, or at least raised, Olivia and her sister.
The Observers either do not exist or are not known to the Fringe Division.
As always, John Noble played Walter to perfection, and Anna Torv was fantastic. However, this was clearly more of a Walter/Peter episode than anything else. I can't wait for next week.