So I'm not a Doctor Who (no time) fan but I am a game dev, so I'll tear you apart on that.
First off, make sure to have the same resolution for both your background and your foreground. When it comes to Pixel Art, having a blurry background and sharp sprites looks... odd.
As for the minigames, I appreciate what you're trying to do but some of the games seem a little unnecessary. What exactly is the whatchamacallit symbol anyways?
The humor was hit or miss. I chuckled at them pointing to the Dalek with their itty bitty pixel hands, but I guess the rest of it was situational. It seemed some of it was taken right out of the script, which you don't have to do, you know. I'm assuming whoever plays this already watched the special, so regurgitating what they just watched is... well, take advantage of your artistic freedom here :P
Anyways, pretty good for two artists.