Overall thoughts on Series 9:
Magician/Witch: I've never been a huge Dalek fan, so the basis of these eps didn't do a ton for me. It also feels like it's filling time with random crisis fairly often (Clara in the Dalek felt a bit contrived). That said, Capaldi, Gomez, and Bleach knock it out of the park (and Coleman does what she can with the material.)
Lake/Flood: I both acknowledge that these were bog-standard Who stories and love them unapologetically. I'm a sucker for base-under-siege monster stories and fun with time travel, so these scratched that itch pretty much as well as they could.
Girl/Woman: On the whole I wasn't super-invested in The Girl who Died, but the humor and the explanation for Twelve's face make up for that. (The face explanation in particular I really do love; it's a fantastic character moment for the Doctor, and its connection to the greater arc being just the thematic irony that breaking the rules and 'saving one person' leads to him losing Clara down the road, rather than being some huge plot revelation, is a relief.) The Woman who Lived was pretty much an excuse to get Peter Capaldi and Maisie Williams bantering back and forth for fifty minutes, and you know what? I'll take that, shoehorned villain aside.
Invasion/Inversion: A pretty low point for the series. While I enjoyed Osgood getting her character developed, and I'll never say no to Kate Stewart (seriously, she's about as good a new series UNIT standby as you could hope for), the majority of the eps are just a not-particularly-interesting invasion story which thinks it's making a deeper point than it is. That said, the climax of the second episode is really something - the idea of war being reduced to two boxes, and Twelve's speech, are so well executed that they almost redeem the rest of the episodes. Props also to Coleman for selling Bonnie as a separate character so well.
Sleep No More: Swing and a miss. Potentially could have been cool, but nothing about the execution landed. Monsters that felt like the bottom of the barrel in "what if ORDINARY THING that you DON'T NOTICE is actually EVIL", secondary characters were half-baked at best, plot was just muddled. I actually don't mind the final twist/ending without the Doctor figuring everything out, but nothing in the ep really earns that.
Face the Raven: A solid ep with a long-overdue return to giving Clara actual character to work with. Agreed with the sentiment that it felt like it should have come right after series 8, and it had to do some straining to remind us of Clara's arc back then. But Coleman and Capaldi absolutely nailed the goodbye, and seeing Ashildr and Rigsy again was fun.
Heaven Sent: Fantastic. A gorgeous setting, superb directing, a great script and plot concept, and of course Capaldi firing on all cylinders. It feels a little out of place in a finale, but I'm certainly not about to ask that we take it away.
Hell Bent: Occasionally rough but ultimately worth it. It was actually pretty well done how they misdirected with Clara in the diner (is she a fragment? Is she amnesiac?), and again Coleman and Capaldi are at the top of their game. The actual business of Gallifrey was fairly throwaway (Saturday Morning Rassilon was particularly odd), but that felt more like them laying the groundwork for future appearances. That said, they could have done more to show why Clara being removed from her timestream was catastrophic; instead they just relied on everyone going on about how terrible it was and how the Doctor was breaking his rules. And let's be real: "if we fly far away enough from Gallifrey, you'll be alive again" is weak reasoning that, even if we're meant to assume the Doctor was knowingly deluding himself, doesn't really make any intuitive sense. But the final stretch ultimately fell back on what this series did best: get Capaldi, Coleman, and Williams talking and get out of the way.
Overall: A bit of an uneven season. I think the two-parter format hurt more than it helped, and the feeling I get for most of the episodes is "there's a few great moments here but not enough that I'd want to rewatch the whole episode." And it seemed like the cast was doing a lot more heavy lifting than usual - and while I loved seeing everyone step up to the challenge, I wish the rest of the show would step up with them. (The arc of the hybrid/confession dial was particularly muddy.)
And Clara. Clara, Clara, Clara. It hurt to see her go; her total tenure clocked in at just under three years straight, which means she's been a contiguous New Who companion longer than anyone else. I also get the feeling that, unless Capaldi sticks along for a good while longer than anyone anticipates, she's going to be the 'definitive' companion of his era. (And speaking personally, the end of 2012/start of 2013 was an impactful time in my life, so I guess I'm a little more nostalgic than most about her introduction.)
But they really had no idea what to do with her until the last three eps, huh? It's frustrating, because her series 8 arc was legitimately well-done, and Coleman's performance has just gotten better and better with time.
Capaldi meanwhile acted the hell out of what he had, but there were oddities here and there with Twelve's characterization this go-around. (I agree with the sentiment that he occasionally slipped towards being Eleven-light at times.)
Still, my ultimate response is: onwards and upwards. Hopefully after what looks like one more "let the actors handle it" at Christmas, series 10 will refocus the writing with a fresh companion.