Another frustrating example of a perfectly good story that just doesn’t click with me, “The God Complex” was written by Toby Whithouse and I wish that I liked it more. I’ll tell you the only thing that I really don’t like, and it’s not Whithouse’s fault in the slightest: I really, really wish that this had genuinely been the Doctor’s farewell to Amy and Rory, and that the characters were never seen again after this. They get a perfectly fine finale once the Doctor gets them out of this hotel, and absolutely nothing that happens with these two after this is better than Amy and the Doctor’s goodbye here.
Fire Breathing Dimetrodon Time 
That was a bit of a problem during the Steven Moffat years, otherwise-good companions overstaying their welcome. First is was Amy & Rory, and then it was Clara. Especially Clara, who I really wish would have left the show a year earlier than she actually did.
Clara’s run is a constant stream of “Is she gone yet?” from me. Her real last episode is nowhere as good as an exit as the three prior occasions where she should’ve gone.