Rewatching the opening sequence again, I do have to wonder about the authenticity of the 1103 year old Doctor.
The lack of a TARDIS is one thing, but note how every bit in that sequence was involving the Doctor trying to evade capture? Furthermore, after the first sequence Amy reads that the Doctor was imprisoned for a day before being spirited away by a "sphere of light", with the Doctor clearly visible as being dragged up towards it.
That doesn't sound like the TARDIS to me. Matter of fact, for some reason the only thing I can think of is a Sontaran ship. And Sontarans equal Clones.
"A Time Lord's Body is a Miracle..."
Hmmm. Curiouser and Curiouser.
...oh snap. Just had a idea. Okay, so we see a obviously recently used table with organic, gooey stuff on it and sitting right next to it is a crate containing Apollo space gear. We also see the TARDIS (Or a TARDIS-like vehicle) from The Lodger.
What if the Little Girl in the Space Suit is Jenny?
"Take away a mans light, his clothes, his food, his friends, his air, and you leave him with nothing but himself. And for most that is not pleasant company."
~ Ramse Truman, "Decending"