We've been to both, and I really thought we would all prefer Flying Fish over Yachtsman. While we enjoy steak, the menu at Flying Fish is just more interesting to us.
But in our experience, the atmosphere at Yachtsman is far more relaxing, the service is better and the food - well, I think the quality of the food at Yachtsman compensated for the fact that the menu wasn't as interesting to us as Flying Fish. Again, I fully expected to prefer Flying Fish - the whole place just seemed more our style - but we were pleasantly surprised by Yachtsman and would definitely return. (For reference, some of our other favorites are Jiko, California Grill, Le Cellier, La Hacienda and Via Napoli.)