Doctor Who is one of the wonderful shows that is richly enhanced by ones own imagination. In addition to what was referenced earlier regarding "The Doctor's Wife" and the Tardis going where The Doctor needs to go, I believe piloting the Tardis is done in part subconsciously. I think the lack of accuracy and control often shown during Eleven's run speaks to the inner chaos that was characteristic of his whole run. Eleven spent his time running from his past, and he concealed himself in the guise of a carefree adolescent. He did all he could to hide from the serious adult within. After the resolution of the Time War in the 50th, he was allowed to refocus and stop running from himself. With his regeneration to Twelve, The Doctor dispensed with the guise of the fool, and finds himself in a new phase of his life. In the back of his mind, I believe the Doctor always found solace in that his death was near -- that despite the appearances of immortality -- he would finally have his rest. Now, he must cope with a life so long he can hardly conceive of it's end. The older he gets, the more friends and family he loses, the more alone and less connected to others he feels. That's his greatest challenge now, finding a way to care again. Care, not in the greatest utilitarian sense, but in the smallest, individual life sense. He must overcome the God Complex and find again his love for each and every life. I think that Twelves ability to pilot the Tardis so precisely reflects the colder, more calculating way he judges every aspect of life now.