We've been to all three. Jiko is probably my favorite of the three - great menu, nice relaxed atmosphere, just an overall great experience. Yachtsman comes in a close second - the menu isn't as interesting, but I think it's a really cozy restaurant and we really enjoy the food. It's so conveniently located (we often stay in the Epcot resorts area) so it's at the top of our list. Flying Fish is good - I love the menu and the location is perfect. But I think the brighter dining room and noise factor kick it down a notch for us. Just not as cozy and relaxing to us as the other two on your list. We also haven't experienced as friendly service at Flying Fish as the other signatures (including Yachtsman, Jiko, Bluezoo, Il Mulino, Le Cellier, Brown Derby, Narcoosees and California Grill), but that can vary anywhere.