I don't see Fringe backing off the alternate universe story at all. I see it being the way they end it. Some how they will either merge the two universes without killing everyone like in the last episode . Possibly using the machine and Peter again. A timeline where Peter never died at all and then there are one Walter, Oliva , Peter , etc and they all lived happily ever after. That is if they have time to wrap up the storyline. But I keep wondering how the Red head running Dynamics, that is acting like Oliva's mother now ,and why she is having Oliva injected with some drug that causes her migranes. Why and for what purpose ? Funny how the changes Peter made in the time line affected both universes and changed things so much in both worlds. The Walternate in this timeline is not as evil as the one before the changes. There are no more references to amber, that the other earth used isolate Fringe events. Is the other earth still suffering from the attacks? Not enough is being showed on these changes in the story.
Also the two Fringe teams are now working together in both worlds and traveling back and forth. This is very much like the story line in D.C. comics that I loved when I was a kid. In the D.C. comics they had multiple earths ,but mainly earth 1 and earth 2 and the older superheros from the 40s and earlier lived on earth 2 and the superheros from the 60s and present day lived on earth 1. They traveled back and forth frequently and worked together. In the "Crisis on Infinite Earths" the worlds were all merged using the Monitor's machines to one consistent universe. The entire history of the earths were rewritten and started over with new origins for each superhero. It was a way to modernize and change histories of the superheros in the late 80s. Some superheroes died ,like Super Girl and some were de-evolved like Wonder Woman and started over completely.
If I were writing this I would do something similar and create one consistent universe for both worlds and create a better timeline using the Watchers and the machine Walter created to do this. I would also fill us in on how the machine ended up in ancient times buried so they could use it now. Also why Walter had pieces of his brain cut out to protect the machine ,etc. I only hope that they do wrap the story up and not leave it unanswered.
