Er, Peter didn't fix both universes. He didn't merge the universes (assuming you meant "merge" as in combined everything about both of them). Like he said, he created a bridge between them so both sides could work together to fix the problems they had created.
I also think that people are taking "he never existed" the wrong way. When the Observer said that, I immediately took it as "he never existed to them, so why would they notice he has gone missing?" In other words, the Observers were able to remove Peter from the timeline (or perhaps the machine did that), but that doesn't change what happened. If you assume that, in the Fringe universe, events are self-consistent, everything that has happened must happen, even if the person who caused it to occur doesn't exist. Obviously, we can't know how or why (right now), but Walter continued his other-universe experiments, which led Walternate to start a war.
Peter still exists, though. He his somewhere, outside of the timeline of the two universes that we have seen. Perhaps it will tie back into who the Observers are and where they come from. Why, or what explanation they'll come up with is beyond me. As soon as Peter disappeared, I made the assumption that Peter will attempt to "come back" or one of the Olivias will "remember" Peter and try to bring him back. The first seems more reasonable to me, while the second feels like something a writer might come up with.