I've been to both twice. At Jiko, both times the meals & service were spectacular. Of course, the ambiance is incredible as well.
My first meal at Narcoossees was fantastic - everything was perfect except for the dessert. The atmosphere was wonderful, we saw Wishes from the deck, then saw the EWP - it was a lovely evening. I was really looking forward to going back. When we went back last year, it wasn't such a good experience. They tried to sit us near the kitchen door, but did move us upon request. Our server wasn't that good, not personable & rushed us. First course was good, our main course (steamed lobster) was awful, dessert was ok. They pumped us in & out in no time. We like a nice relaxed, leisurely meal at night. It was one of our most expensive meals of our trip & it was the worst.
Based on that, I would do Jiko again, but probably will not risk Narcoossees again. It's an expensive gamble IMHO.