1-THE ,SO-CALLED "DARK" DOCTOR
For example, when Ten saves everyone on the Waters Of Mars and says he is Timelord Victorious,we are suppose to believe he is becoming EVIL when all he really did was pull a Marty McFly and prevent unneeded deaths(like Adelaide who could as he said just inspire her granddaughter alive),the fact that he wants and does wipe out Daleks is portrayed as wrong in Journey's end when he dumps Meta-Crisis on Rose...except for the fact that they are genocidal space Nazis that all without exception want to exterminate innocents.We are meant to see the War Doctor as a monster when he prevented the Time Vortex from being destroyed by killing the Timelords who wanted to commit genocide on a universal scale.
I have no problem with a hero that isn't a Light Yagami,a Walter Whiter or a Dexter.But the Who writers desperately want to convince that the Doc is repressing that needs his companions when a lot of his acts just fall into Designated Evil.
2-Timey-WimeyDidn't the Time Of The Doctor create a paradox by not having the Doctor die definitively on Trenzalore ? Clara pretty much saves the Doctor because she knows he's going to die because she has been to his grave with him and if he doesn't die she couldn't have been to his grave,a principle already explained in "The Angels in Manhattan",i.e. can't change the past using future information from the current time line.It seems the show plays a very strange game with changing time.One second you can't like when you save Rose's dad,but after in Journey To The Centre Of The Tardis or in the Christmas special from 2012,you can.
What the fuck happened to the Reapers and time collapsing on itself?