There shouldn't be a Ronin in a three player game, it's a shogun vs two ninjas with some added bonuses for the shogun. Page 8 of the rules outlines the special rules for a 3 player game.
That being said, I haven't played the game three players, so I can't promise you it will be awesome, but it does appear that it should at least play a lot differently than your first attempt. =)
My bad, I guess my friend had decided that is how to play 3 players, either because he didn't bother to look it up properly or decided he didn't like the official rules.
Having now looked at the official rules, I must say it is even worse really. The Shogun should never win unless the ninjas are terrible. The Shogun could get an occasional kill, but I don't see how they could ever keep up with the ninjas, and further, the ninjas will just make sure that neither of them dies by trading back and forth honour as needed. The Shogun will always have far too few cards to do anything and getting double end game points is useless as they will always be the one to lose all of their honour to end the game.