I don't think the 2-vs-1 scenario is all that big of a problem in 3-player
games, since if one player begins to pull ahead, it only becomes natural
for the other two to ally against the leader.
One problem in 3-player strategy games I've seldom seen solved though is
the kingmaker problem. Suppose one player is losing hopelessly, but is
either able to hurt one of the other players enough on the way out to give
the other one the game, or is able to determine the winner more directly
(by deciding whose mating trap to walk his king into...). Then the winner
ends up being decided not by who played better, but by whom the _loser_
was feeling better disposed towards.