There's no doubt that from a physics point-of-view, the strongest paddler should be in the bow and generally in a mixed pair, that will be the guy.

That doesn't address the control issue, though.  Lot's of guys have trouble giving up control to the better half, especially in a "manly" pursuit like wilderness canoeing.  And even if the guy is willing to give up control, his partner needs to be willing to take that control as well.  That is nearly as big of a stumbling block to many pairs as the first issue.  Navigation can be part of what makes it a stumbling block, of course.  Most tandems delegate that aspect to the stern paddler as he/she needs to make the decisions and course corrections necessary to get where you want to go.

Bottom line, there is a lot of psychological and social barriers that must be overcome to pull off the pairing that physics might dictate to be the most efficient.

My wife rarely paddles with me anymore but when she did, she always paddled bow.  Physics-wise, we'd have been better off with her paddling stern.  However, she doesn't have the confidence in her navigational or steering abilities required to be truly comfortable back there.  Physics lost out to both of us being more in our comfort zone in other ways.