In the Google+ Fate Core group, there were a few people that did a Dr Who game for the anniversary. Maybe they can give you some pointers on what they did.
Time travel is a pretty fickle thing in story telling. The most important part is to set some ground rules about how time actually works. Can you go back and change anything, get back to the present and live in the changed live? would you remember? Would you be changed as well? Are there things like "fixed points" that can't be changed? Is there one timeline? Multiple timelines? What about trousers? Once you set down the ground rules of what is and isn't possible with time travel, it's going to be easier to play a time travel game.
And still, time travel games leave the door open for Bill and Ted style maneuvers. You can do a time travel magic maneuver that places a speeding truck on the street you are fighting on, because you are driving the truck yourself, because at that moment, you plan on going back after the fight to drive a truck along the street to help out past you. Only this can lead to paradoxes, since you might have lost the fight, if you didn't go back and drove the truck, and then you couldn't have gone back and driven the truck. It can get... complicated.
