I don't think that AUJ is better than DOS just becouse it has a stronger thematic spine. After all, AUJ also feels to me more like part of a bigger whole than a stand alone film. Personally, I would put both movies as equals, one trading whimsical pacing for more awe inspiring attractions (Smaug). The end effect is more or less on the same level.
This is why, despite my many complaints about the new trilogy, I still refrain from putting a score on those films until I see There and Back Again. Both AUJ and DOS work for me like single episodes of a tv mini series. They are even less individual stories and more "parts of a bigger whole" than LOTR was 10 years ago. I think only after seeing the whole trilogy, can we talk about the efficiency of PJ new vision (though obviously there are some elements that can be easily criticised or praised, no matter how TABA will close the series).
Plus, there are some changes and plays on the story made by Fran and Peter, that are generally disliked by people, but have the potential to really come into their own, once it all reaches its culmination in part three. While there's no doubt in my mind that this new trilogy is a whole level beneath the old LOTR and that Jackson is no longer the director and screenwriter he was 10 years ago, but generally despite all the current whining, I really think this trilogy has a chance to be better recieved in hindsight, once people can appreciate it as one story.
A year ago I used to whine and ***** about the pacing and the thematic and dramatic "emptiness" of AUJ. But now watching the extended edition on my couch, under a blanket with a hot beverage and snacks withing hand reach, is pretty much how I would love to spend one post-christmas evening