Just caught up with this ep. It certainly felt like it was meant to be the season finale. I found it rather predictable, but because it was so well acted I didn't mind. I'm not sure why people have a problem with Jones' plan. That was one of the things I found predictable. I mentioned earlier in the thread that Jones probably wanted to blow up the bridge so that the two universes would be destroyed, and that he would be safe on a third one.* I didn't however connect the Westwood ep with his plan - that he was creating a "safe" zone that would remain after the two universes were destroyed.
It was kind of ingenious that Jones was using the cortexaphan kids to do his dirty work, but not unsurprising since he spent most of Season 1 going after Liv. And it now makes sense why he was dosing her in the current timeline. Though if she wasn't needed to complete the plan, I'm not sure what else he might have been dosing her for. And as mentioned above, I liked the call back to a previous episode where Lincoln recognizes Nick.
It was also very predictable that Lincoln would stay with the Alt-Fringe team. But since they didn't have much for him to do on our side, that's ok. My only disappointment is that destroying the Bridge didn't "reset" the original timeline. This incarnation of Walter has come a long way, but the old one had years to get over his agoraphobia and connect with the Fringe team. I feel like the rapport isn't quite where it was. And Liv magically regaining her memories continues to be a huge thorn in my side. That said, Peter didn't actually get in the machine so a major reboot seemed unlikely.
In any case, I'll miss the alt-Fringe team. But I'm ready for a new phase in the story. We have the gang back together (in a slightly different way) and I'm ready to hang out with them for awhile.
*But I formulated this opinion after he asked alt-Broyles to plant the device that would retune the two worlds. Thinking about that ep now, it seems odd that Jones' plan now involves the cortexaphan kids as the returners. Either Jones had incredible foresight and worked on two master plans simultaneously or the writers' didn't think we'd make the connections.