Eh, the ending of No. 6 was kind of disappointing. It fell into the same trap as Fractale of starting out great, stumbling up on the pacing, never quite getting it right again despite some flashes of greatness, and delivering a decent ending that fell kind of flat because the build-up just didn't do it justice. I think my main problem is the mythos of the city No. 6 just wasn't developed enough. What they were going for reminded me of Sora no Woto, where the details of the history weren't terribly important, and it was more about the universal feelings and themes upon which it called. But despite Sora no Woto's heavily slice of life episodes, it set the mood perfectly, and gave me an innate sense and feeling about the world in which it was set, which I never quite got from No. 6. It's not even that there weren't plenty of hints or plenty of great tone-setting scenes; they just didn't match up very well to give a cohesive whole strong enough to carry the ending, resulting in a finale that might have been well-executed given a better build-up, but the mythos just wasn't there to make it work.
Overall, I think I'd have to say that pacing is the biggest stumbling point in all of the noitaminA series that don't quite succeed, where everything else tends to be very well-executed.
ETA: I'm happy to say that Usagi Drop does not fall into this category. The only disappointment was that it was only 11 episodes.