The big question in every fans mind is "How can Amy have a baby with Time Lord DNA?".
Moffat may have been dropping hints since Series 5.
What makes Amy special? Here's a list:
- Amy grew up with a Time Crack in her wall, the universe pouring through her mind and body. This point was made in the Series 5 finale 'The Big Bang' by The Doctor himself.
- Amy Pond has traveled through time in the TARDIS. In the episode 'Flesh and Stone' Amy asks The Doctor how she can remember the Weeping Angel that was in her head if it ceased to exist. The Doctor answers that she is different now that she has traveled through time in the TARDIS. She can remember altered time lines.
- Amy was locked in The Pandorica's regenerative field for 2000 years. The same Pandorica The Doctor was previously imprisoned in. Amy was ressurected by the regenerative field of The Pandorica. Perhaps it altered her DNA as well with DNA of the previous inhabitant (our favorite Gallifreyan).
- She conceived a child while traveling in the Time Vortex. An event that may never have occurred before, given the fact that Time Lords didn't travel in TARDISes for long periods of time and as a race 'quickies' seem uncharacteristic.
- And then there may be an event that Moffat has yet to share with us as we still don't know when Amy was taken.
So in conclusion, it seems unlikely that humans just having sex in the TARDIS would result in a 'Time Lord' child. However, as The Doctor has stated on many occassions, Amelia Pond is 'the girl who didn't make sense'.