I would say that the JAL food is better than the ANA food. Service is maybe difficult to compare for me, as I am one of the passengers clearly highlighted on their tablets, but I would say I generally prefer the JAL service in any class.

Seats are a bit of a random mix, I am not particularly opposed to SSIII as long as I don't get a middle seat (D or G). I also don't mind business staggered as long as I can get a true window seat, but it does make my seat selection quite narrow. But, I'll not complain in either option even if I don't get my preferred seating option. For the connecting flights, NEO is good for a day flight and less than ideal for a night flight, though row 1 or 7 helps a lot for night flights. Business Cradle is just terrible no matter what. For JAL you may hit some APEX Suite flights, which is a lot better than all the other options mentioned so far.

The JAL Sakura lounges in Haneda and Narita are probably better than the ANA lounge, the JAL first class lounges are clearly ahead of the ANA Suite Lounge. There are plusses and minuses for both the Sakura and ANA Lounge, so only probably, and some will prioritize differently and prefer ANA. If you can get a Haneda T2 international departure, it is an even closer call. The Haneda T3 ANA Lounge seems as crowded as ever, even if ANA has moved a lot of flights to T2, but they also cut T3 lounge capacity at the same time. I don't think the JAL lounge gets as crazily busy, but I am not a frequent Sakura lounge guest, so I leave others to come with more accurate statements on that.

Bedding and lounge, United wins clearly. Staffing can be hit or miss. Food is well below both ANA and JAL, and so is service.

If JAL is even the cheapest option, there should not be much to think about in my opinion.