Flying Fish is part of
Disney Dining Plan, therefore, it will always be more crowded and hectic.
On the other hand, Blue Zoo is not part of Disney Dining (but takes Tables in Wonderland, if you have it) and is far less hectic.
Blue Zoo, in my opinion, is the best restaurant at Disney (unless you want to wear a jacket & tie at Victoria & Albert).
First of all, the Bread Basket with Fennel Butter is spectacular. Yes, a simple bread basket.....and it gets better.....cutting-edge fare along with top-notch service, an excellent bar & better kitchen....and world-class desserts!!
If you're a Foodie, Blue Zoo can offer a wonderful experience; I would never say the same thing about Flying Fish.
Flying Fish is very good, but I could never imagine saying that I had a truly memorable meal here.
I go to both as often as possible, but Blue Zoo is certainly the favorite in my family.