In last night's episode, Agent Broyles wondered why pieces of Walternate's Doomsday Device are in our world. Later, we saw Bolivia communicate to her superiors in the alt-world that Peter was "engaged" and that he'd found the "first piece."
That raises an interesting question. Are there two doomsday devices? Perhaps Walternate knows this and is manipulating Peter to destroy our version before we can build it.
I like this possibility because it sets up an interesting dilemma for Peter. If there are two devices, each with the ability to destroy the other universe, then Peter gets to choose which universe survives.
Is that why he's so important to the Observers?