Settlers of Catan explicitly requires 3 players, in fact. I'm not terribly surprised it doesn't work great with 2.

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.