It's quite unfortunate to realize that this is, more likely than not, the series finale. For all that it resolved some of the open questions surrounding Catherine Weaver and her goals, it was clearly meant to be a springboard to a new and even more complicated arc for a potential third season. As such, this is going to be one of those shows that will probably end incomplete, much to the frustration of its loyal audience.
And that loyal audience will be frustrated endlessly for many years to come. Not only will the fans have to accept that the show is open-ended, but they will have to put up with all the late-comers who, despite the many online sources available to them, will simply assume that the producers and writers chose to leave the series on a cliffhanger because their DVD set or download description says "series finale". (Doubt me? Look at the fans of "Stargate Atlantis", and how many people based their "series finale" without bothering to realize that the series was cancelled after the entire final season was already in the can! But I digress.)
For the most part, the episode unfolded just as one would expect it to unfold: Sarah was rescued in a rather public manner, and Weaver's endgame was exposed. Sarah's rescue was a bit more overt than I had expected, actually, and gave those looking for some serious Cameron action a nice parting gift. I can only imagine how much the finale cost them in the end!
More importantly, the finale never quite let go of the titular focus; a lot of time was spent on Sarah and her situation. Not just her incarceration, but rather, her overall health. John was left wondering if a damaged nuclear power core from a terminator could, over time, cause cancer. It's not a silly question, but it does lead to one of the most sexually charged moments in the history of the series. That it was essentially glorified hardware maintenance makes it even better.
The bottom line is that Cameron has, one way or another, gotten under John's skin. He's willing to do whatever it takes to restore her in the end, which is not particularly the smartest move. In fact, it's hard to argue that it's a necessary move. Which is why it's surprising that Sarah didn't try to talk John out of leaving with Weaver. They had very little reason to trust Weaver, after all, and considering how important John is supposed to be to the survival of humanity, letting him leave to times and parts unknown seems unusually out of character.
That said, the plot twist/cliffhanger seemed to be designed to demonstrate why John Connor specifically needed to be the one to lead the fight against SkyNet. John and Weaver follow John Henry into a future where John wasn't around to organize the resistance. This would likely be the future created when John left with Weaver in the first place. Where that would lead/would have lead to is practically impossible to predict, but it would have allowed for more time with Derek, Kyle, and the original Allison from Palmdale, so it couldn't have been bad.
It also would have likely been temporary, and explored concurrently with whatever Sarah and Ellison wound up doing in their own time. Under the circumstances, it seemed like John Henry was doing something very specific at Cameron's request. Perhaps this is related to all the glimpses we've had to a future where John Connor is an unseen leader, with Cameron and others apparently in charge. It's hard to say, because we're left with only a glimpse of what the writers had in mind for the future.
There were a number of loose ends left by the end of the season, particularly in terms of the many timelines in play and how it was all meant to fit together. The final twist promised to shed light on some of those loose ends, so it's all the more disappointing that the series might end on that note. That said, it can't be claimed that FOX wasn't patient. They gave the series an entire second season, when they could have easily