Settlers is a poor 2 player game: It's really designed for more. Then balance comes form bashing the leader mechanisms: Unfavorable trades, robber uses always hitting them and so on.
You can apply The Settlers of Zarahemla setup and trading rules to Catan (while avoiding the additional mechanics in Zarahemla) to create a 2-player Catan. It does have the problem xivzgrev mentioned if you do not each secretly adopt different atypical strategies each game.
