I know opinions vary, but I really think Moffat did a great job with the dynamic between the Doctor, Amy, Rory, and River. He built his own little world within the greater Doctor Who universe. Once all those things went away, however, I think he had a hard time capturing that magic again. He had to continue with new characters (including the new Doctor), but I don't think he had as clear of an idea of what to do with them.
There is an awkwardness to Series 8. Individually, I think Capaldi and Jenna did a great job, but there's something about them that doesn't quite fit in with the stories being told.
I've said this before, and I'll say it again here: even though by the end of this year Jenna will have done 2 series with Capaldi vs. 11 episodes with Smith, it's her time with Smith that I suspect I'll remember most. They were a perfect Doctor/Companion pair. 7B was the last time I remember enjoying the show so much I couldn't wait for each episode. I did miss the Ponds, but that was erased pretty quickly once Eleven and Clara got going.
I think Moffat misfired when he created conflict between them. It has nothing to do with Capaldi and Jenna personally. They do work well together. They have chemistry all their own. But creating friction between them and doubt in Clara's mind just wasn't the way to go. I get that you had to change the dynamic. You couldn't have constant flirting between them as if you still had two actors close in age. But Moffat could've made Capaldi's doctor more of a professor type, kind of impatient, just not as cranky. A little personality tweaking is all that was needed. The "change" between Doctor personalities from 11 to 12 didn't have to be so drastic, to the point where it affected his relationship with Clara.
It's like he had one of those apps from the woman in Bells of St. John. He put some of the settings too high on this Doctor's personality, and made a bad choice in taking an entire series to have Doctor and Companion find their groove again. When there was no real reason why the should've lost it in the first place.