I liked the finale. It actually offered closure. I liked that reframed Spock and Kirk getting along so well. I liked that it justified Pike's acceptance of his fate (although, maybe it would have been better if he wasn't so accepting already). I liked the explanation for why Captain Batel is not in TOS.
My least favorite in S3 was Four-and-a-Half Vulcans. That one could have been done better, and there was already too much body swapping.