I'm starting to wonder if I completely misread the ending, because I haven't seen anyone mention what I thought happened (yes, I read the thread) and if I'm right, then all the things so many viewers are unhappy with about Clara are actually deliberate choices on the writers' part. When The Doctor was looking at her all suspiciously at the end, and then claimed that she had been an exceptional Doctor and goodness had nothing to do with it, it's because he knows there's something off about her--which is basically what Missy's subsequent moment a second later confirmed. Clara's complaining about all this stuff because she really DOESN'T want to be traveling with the Doctor, she'd much rather be with Danny back at the school, but Missy has done something to her that's compelling her continue traveling with The Doctor so she can continue serving as Missy's plant so Missy can spy on him. That would make sense with last week, where it seemed to be leading to Clara leaving at the end...and then she didn't, for no discernable reason. Because Missy's done something to make it so that she can't. And now The Doctor's seen something in her behavior that has shown him something's off about her.
Anyway, maybe this should be in a speculation thread (I don't think there is one), but that's how I read the ending. (And no, I don't have any spoilers or anything.) But the writers making a companion who's being compelled by outside forces to travel with him against her will makes more sense than just a whiny one who doesn't want to be there, but won't just cut the cord, IMO.