I think I finally figured out what's been going on with Fringe this season. It has to do with the fate of Peter Bishop and it fits in nicely with my obsession with geodesic domes.
Peter Bishop is a lab rat.
Pinker and Wyman have been telling us lately that the answer to where Peter is has been staring us right in the face all along. My guess is that the Observers, who are scientists from the future, have created a pocket universe for Peter to live in so they can observe his reaction to events so they can successfully map out a future timeline where everything falls into place. No more mistakes, no more wars and no more inter-dimensional damage.
A pocket universe is described in Wikipedia are "fictional artificially-created universes that exist within the bounds of another universe. The term pocket universe is derived from its illustration in the actual universe where it is usually portrayed as an orb which would fit in a pocket."
What better place to observe and conduct experiments on our hardy band of brothers (and sisters!) than in a laboratory setting. The geodesic dome is the perfect illustration of a pocket universe so it is no wonder we have seen so many references to them this season. This may seem a little cruel to have Peter and the others but it is better than continually disrupting the universe and or timelines trying to fix what the Observers have gotten wrong.
Pure speculation on my part of course but it sounds fun and I hope to fill this theory out as my thoughts clarify.