All of my flying in Japan on ANA, JAL, and Skymark has resulted in quite full flights. But, I'm sure (as it is with a particular train that leaves Hakata at a certain time that is usually fairly empty) that every once in a while there is a plane that is semi full.
I have flown in both ANA's -400D and JAL's -400D. Service is, as mentioned, bare minimums for an airline outside of the USA (however even THIS service is a far cry above many carriers in the states today). JAL's -400D was fine, but ANA provided me with a much better inflight FA
service. My experience with both airlines is that ANA is a bit more attentive to passengers, where as JAL can be downright passive at times.
I go to the Fukuoka Airport once a month (due to go there tomorrow in fact, 11/6) to do some spotting and try to get a few good shots (my shots are never good enough for this site, but for others, they are). And, as soon as the -400D's come in (ANA and JAL fly their -400Ds back to back sometimes, which is great to get a "second chance" if you miss the picture), it seems like they just got in before they're taxiing back to the active to depart again. They're on the ground for an hour or less, and that's it. I've watched them from the observation deck at the airport in Fukuoka. The pilots even stay in the aircraft. The pax get out, the service trucks come in, baggage comes out, new bags go in, pax board, the catering truck leaves, tug pushes the plane back, and that's it. Once in a while I'll catch the plane getting fueled. But, they mean business.
As for my seat experiences, I prefer the -400D over JAL's 777-300 domestic, however I did have the chance of flying the daily NRT
flight once, where they suddenly (to my suprise) upgraded me to business class free of charge. This was on a 777-200 outfitted for international flights, and was very very VERY nice! As some people do know, JAL has their new J-class, which is 1,000 yen above your ticket price that you can pay at check in (about 10 USD) to upgrade your seat. Not bad, really, but ANA's Super Seat makes JAL's J-class look like UAL's enhanced Y class seats.
Then again, there is always Skymark, which seats 2-4-2 in a 767...and the seats are smaller than a Northwest DC-9 window seat...myself being an "average" sized American, I can't find myself comfortable in any Skymark seat except for their business class, of which you can upgrade for about 4,000 yen (40 USD) at check in, of which I HIGHLY reccommend. If you buy a Skymark ticket around two months in advance between Fukuoka and Tokyo (or vice versa) it'll only cost you around 1 mon yen (100 USD). If you buy with other carriers (such as ANA or JAL), it'll cost you.