So, I'm rewatching some of Smith's earlier episodes, basically series 5 and 6, and does it weird anyone else out with how they seem to tease the Dr/Amy relationship, especially with regards to Melody/River's paternity?

I think AGMGTW is the worst culprit of this, with Amy's speech that opens the episode, and then Vastra's questions later. Amy's speech is obviously playing a little joke on the audience, using language that could apply to both The Doctor and Rory, but more accurately just the Doctor. I suspect the "punchline" is meant to be the bit where Amy says "he's your father", by which I mean that I think that's meant to be the point where the audience realises she's talking about Rory. The trouble is, the show had created a narrative where that's not necessarily true, and we only realise (or at least, I only realised when I watched it for the first time all those years ago) that she's talking about Rory when he appears on screen.

There's also the fact that the Doctor replies "It's mine" to the question about the cot, in such a way that it makes it seem as though he's talking about Melody. This, again, is a bit of a joke, but not a particularly funny one.

And the Doctor does get very defensive when Vastra asks if Melody is purely human. More defensive than he should have been if there was absolutely no chance that she was his child.

These, and other signs throughout series 5 and 6, seem oddly adult for what was, and still is, ostensibly a family show. We all know Moffat was basically writing one-handed, but this always seemed a little less sexual and more creepy and dirty to me. To be honest, Amy's obsession with the Doctor always seemed a bit odd, from her running away with him on the night before her wedding to her wanting to kiss him at her own wedding reception, in front of all her friends and family, and her new husband.

Basically, I think Moffat thought he was being funny by implying that the Doctor might be River's father, but the problem was that he had made it too plausible a theory. If it had turned out to be case that he was River's father, I don't think anyone would have been that surprised, or at the very least it would have had the ring of truth to it.

Did anyone else feel the same way?