Well, that was fun
It looks to me like Moffat has decided to simply ignore the Time War backstory that was so much a part of Eccleston's and Tennent's doctors. That he should be so outraged at the attrocities committed by the alien doctor, without even making a reference to his own similar actions against his own people in the time war struck me as a false note.
I'm assuming that it was a conscious decision on Moffat's part to ignore that material, since it was so obviously available and applicable. I wonder why?
My wife suggested that the when the alien doctor talked about the rage in the Doctor's eyes and compared the two of them, he was making just such an allusion, but I thought it was a pretty thin attempt, and wasn't followed up upon as it absolutely should have been.
The suggestions of similarity were far more than a thin attempt - they were blatant. Moffat pretty much spent half the episode talking about the Time War and The Doctor's actions in it and the guilt he feels for them.