if Clara seemed to be channeling Amy in Gaiman’s story, it’s because she was Amy. Neil has said that the worst thing about writing for Doctor Who (apart from the pay being low) is that just as a script is finished and done with, news arrives that the main companions have changed and it needs to be rewritten - in double quick time, and no extra fee.
Personally i think Moffat’s stories are among the best, but he’s probably not the best man for the helm.. However, I do think he’s done a better job of it than Davies did. I know that’s controversial, but i didn’t really like what RTD did with the show.
I have mixed feelings about Riversong. very well portrayed by Alex, but the character is too much of a Mary-Sue. I don’t think we have seen the last of her - her parting shot hints that she know’s a little more of the Doctor’s future, suggesting he still has another adventure or two with her earlier self.
I liked Matt Smith’s portrayal as the Doctor, but I had a feeling he would leave the show after this season, and it is probably the right time. Doctor Who is not a soap, and picking the right moment to leave is crucial to his career.
One thing that both Davies and Moffatt have done that harks back to the very genesis of the show is to underline the basic truth that it isn’t all about monsters and a strange man in a time machine - it’s about the companions. Though i do wish that every new companion is not ultimately revealed to be the “most important person in the universe” - it’s becoming too much of a cliche.