Both are very good. Jiko is currently the critics choice and has a loyal following because people sense something different, even if it is just smoke and mirrors.
IMO, FF has been the best Disney run restaurant year in and year out. They have the best steak on property (IMO) in the charred NY Strip but if you prefer a filet that can be cut with a butter knife then JIKO wins. FF wins the seafood battle as they have a bigger variety in their offerings and JIKO hasn't been able to adequately replace their 'signature dish' (which WAS the monkfish) in an acceptable fashion, again JMO. Jiko wins the salad/appitizer battle by a nose (thanks to the flat bread) even though they callously discountinued their hands down best app (duck and pork firecracker) a couple years ago.
The atmosphere is quite different. JIKO is subdued and generally quiet and certainly more romantic while FF is a bit noisy and festive.
I have always found FF's service to be far superior to JIKO but I've heard tell of some great servers at JIKO, I've just never experienced them.
Good choice both...