I don't understand what people don't get about the farewell between Clara and the Doctor. They both realized the other one was lying, but also both realized the other one needed to. To have a reason to stop traveling together. Clara can't do it anymore emotionally, but she can't hurt her friend. The Doctor sees that Clara is hurting, but is to scared of being alone and leave as well. This was what they both could use a reason to split up really.
And that last line of the Doctor..... 'Why do people hug?' They would both see the truth in eachothers eyes.
Sure, there was some bad stuff in this episode. But nothing's perfect. Not even the best episodes of your favorite show. Looking at this as a complete season, hits and misses all around, but the biggest thing I got out of it was a great Doctor, played by a great actor.