Okay, here's an in-depth review of all locations. (Spoilers!)
I really liked the Tardis. That has to be the best minecraft version I've seen. However, the library thing above it confused me, and I never did use the lever.
After leaving the Tardis and boarding the ship, if you go to the room on the left there are two spacecraft you can get stuck in very easily. Also, on Level 1, when boarding the pirate ship, it's very easy to fall off the black wool and get stuck there, especially since you're teleported facing the drop as you walk off. Overall, I really liked detail put into the ship.
On the pirate ship, the elevator has visible redstone which I think detracts from the experience a little. The detail on this ship was excellent as well.
However... the Xenon Moon wasn't very good. Sorry. It looks less like a moon, more of a redstone testing flatland. It was a little hard to find the book, because I wandered off and didn't notice it. The cliff faces around the crater should be a little steeper; maybe the crater should go into the ground more. I also like the ship escape, but the lever for the FTL drive was already pressed down when I got there which I thought was a little odd. If it was powered, why wasn't the ship blasting off to space before I arrived?
As you reach the pirate captain, the message "Challenge: Fight the Pirates take the Pirate Captain's Head back to the TARDIS!" doesn't sound very much like the Doctor -- could you imagine him saying that? I killed the pirates anyway, but nothing happened. I like the escape pods.
Throughout the map, there was a little too much running. I know that's all that the Doctor seems to do sometimes, but there should have been at least one thing that the player should have had to stay in one place for. Otherwise, it seems just like a 'walk through this pretty scenery' type of map. Maybe a puzzle of some sort? Also, you might want to do /gamerule commandBlockOutput false, so that you don't hear all the teleport messages going off.
Anyway, great map. I'm not trying to put it down with my criticisms, but it could be an even greater map. I hope you take a few of my suggestions

.