The move to Vancouver was the missing link here- the cold, hard, soul-dead streets of Manhattan saddled the show with a depressing glaze that inhibited its humanity. The lush haze of Vancouver and those ever-changing skies are a narrative opiate - it feels like the show is finally where it belongs.
The show's dynamics are evolving as well- Fringe is less centered on Olivia in favor of the thorny father-son relationship of Walter and Peter, but everyone's acting game has been raised exponentially since season one (even Agent Farnsworth, whose character has been a bit of a cipher heretofore).
The Fringe mytharc really gets under your skin, with its interdimensional war storyline played out in consensus reality. You totally buy it, which is the acid test for any sci-fi with legendary aspirations. And the less Fringe tries to play like The X-Files, the more it feels like it.
Particularly that sense of anything-can-happen and that whoa-where-the-hell-did-that-come-from vibe that the TXF's Vancouver years wielded so well. And this standalone-within-the-arc format is really something that the sci-fi soap operas should pay attention to. Well, should have, more like it- most of the them are going or gone.
Advice to aspiring showrunners: never-ending serials are for soaps. And they're all dying off too.