There are two simple ways to consider this episode. The first is the most positive interpretation: this is the culmination of everything the writers intended concerning Agent Scott and Olivia's absorption of his memories. The second is the most negative: that this is the writers' attempt to bring resolution to a plot element after realizing that they didn't know where to go with it.
As much as I'd like to trust that Abrams and his writing staff knew what they wanted to do with Agent Scott from the beginning, this felt a little too pat for my tastes. The only thing that keeps me from subscribing to the theory that they fudged the resolution is the nature of any network freshman series. Networks generally pick up new shows for a total of 13 episodes. The "back nine" comes after the first several episodes prove the viability of the series to a sufficient degree.
As a result, a smart production staff will develop a basic arc for those first 13 episodes, while introducing enough material to give additional episodes a strong foundation. And that could explain why the Agent Scott elements came to a rough conclusion in this episode. This would have been among the last episodes produced if the series had not been given a "back nine".
That said, I liked the idea of Olivia's psychology being hard to fathom. I thought it was a compelling complication to have doubt regarding the origin of Olivia's thoughts and actions. And considering how often Walter mentioned the danger of going into the tank, and impossibility of communicating with John in the "memories", there should have been a more compelling payoff.
This situation does confirm the nature of the relationship between the Fringe Division and Massive Dynamic. Since we already have sufficient evidence that this connection is questionable at best, it lends credence to Olivia's suspicions that there may not be a right side to this particular war.
It also introduces the notion that other branches of the government intelligence community have teams working to understand and combat The Pattern and those taking advantage of it. More importantly, this effort seems to have been, more than anything, an attempt to mitigate the civilian casualties of this war.
Olivia and her team still have a particular role in the ongoing struggle, even if its nature is changed by this episode. Walter is connected to many of the players (probably on both sides), and Peter could be a product of precursors to The Pattern. Olivia seems to be desired on both sides, for reasons that have yet to be revealed. I'm sure the rest of the season will delve into that aspect of the show, but I'll still be a little disappointed that Olivia's memory problem was so easily resolved.