See also this:

I wouldn’t hold your breath on why he remembers but others didn’t, because I’m pretty sure there was a one-or-two line explanation from Eleven to Ten during “Day of the Doctor” on that subject.

I’ve mentioned it before, so pardon if I’m repeating myself too much: I think an MCU version would be (heh) fantastic if it were done as a mid-Sixties period piece that focused more on cosmic threats.