There's really very little between the airlines in Japan; they are quite expensive, but the courtesy, cleanliness, efficiency and general impression are all superb. I flew with JAS from Osaka to Fukuoka in March 1999, my first MD90 flight and it was excellent.
The captain took a digital photo of me in the cockpit and sent it to me by email later! (This was about two months before cockpit access was stopped, after that maniac killed an ANA 744D captain).
I'd certainly fly with them again.