I didn't say he needed a male companion. He could be gay and still travel with a girl. You could make him gay and give Captain Jack a reason to come back! Wouldn't that just make his day?
And the Colonel Runaway scene from "A Good Man Goes to War" is all the evidence you need that Matt Smith's Doctor has a dark side.
Also, the flesh two-parter, where he manipulates the ever-living-fuck out of Amy.
Smith's Doctor was typified by a superficial lightness and absent-mindedness that concealed a pretty nasty character.