1. Silence will Fall
Matt Smith’s first season as the Doctor is easily the best year of Steven Moffat’s time as showrunner. The cracks in time, created by the exploding Tardis, was a great hook and made for some exciting storytelling. Except if the Silence wanted to stop the Doctor from destroying the universe, why did they destroy the universe? I’m sure there is a timey wimey reason for this, even the show’s villains don’t realise that trapping the Doctor in the Pandorica makes it happen, but it still doesn’t make a lick of sense.
2. A Fixed Point in Time
The Doctor was supposed to die at Lake Silencio at the hands of River Song. It was made clear at many points in season six that this event was a fixed point in time and could never be changed. Except the Doctor just hid in the Tessalecter and was barely singed by River’s supposedly killing blows. This is a cheat, which is fine for the Doctor, he cheats death for a living, but the rules that Russell T Davis set up about fixed points in time, which is used to tragic effect in The Waters on Mars, is thrown right out the window.
3. How did Clara escape the time stream?
At the end of The Name of the Doctor, Clara is trapped in the Doctor’s time stream after deleting the Great Intelligence from the Doctor’s timeline. She is saved after the Doctor jumps in after her, while also getting a sneak peak at John Hurt as the War Doctor. How did they escape? Is there a clearly marked exit point? Now that you mention it, how come we never ran into other versions of Clara after wards? That would have been trippy as hell.
4. The Problem with Listen
Listen is a classic episode of Doctor Who, no one is arguing that, but what’s with Orson Pink? The Doctor and Clara meet the displaced time traveller at the end of the universe, and it’s hinted that he is a descendent of Clara and her boyfriend Danny Pink. The only problem is that Danny died at the end of the season, without having any children with Clara, or anyone for that matter. That means Orson Pink is wiped from existence, meaning that Clara is never given the toy soldier that she gives to the young version of the Doctor.
5. Rules are made to be broken
Finally, Steven Moffat leaves the show by breaking one of Russell T Davis’ time travel rules for the final time. The main motto of Moffat’s time running Doctor Who is that time can be re-written, which is what happens when the 12th Doctor saves the Brigadier’s grandfather. It’s a great send-off for Peter Capaldi, but it goes against the logic set up in one of the best episodes of the T Davis era, Fathers Day. In Fathers Day, Rose saves her father from being killed, going against history and creating a wound in time. This leads to the reavers eating people until Pete Tyler realises he has to die again. Where are the reavers for the Brigadier’s grandfather?