I've been playing a lot of Ys 2 player lately and it works fairly well. In the rules under the 2 player variant it says to use a neutral player with a value of 0, 1, 2 and 4. It goes on to say that you can increase this with skill level of the players. I've found a very effective set of numbers is 1, 2, 2, 4.

I always play with the "King's Favor" variant when playing 3 or 4 players but the rules state you don't with 2 players and I miss that but see it as understandable. However with the above distribution I've found you can effectively keep this variant in the game as well.

Take the rest of the neutral player's brokers and put them face down next to the board. At the end of each turn randomly select 1 of the neutral player's unused brokers and place it in the court. This creates a very nice mix with 0, 1, 3 as possibilities of brokers going over there. It's been interesting so far.