Just completed an Asia trip in JL's Executive Seasons Class, using an AA mileage award. Below is my comparison to AA's transpac biz service

Seats
JL Shell Flat Seat vs AA 777 biz seats. Advantage JL
At first the Shell Flat seat doesn't appear to have as much pitch/room as the AA seats, but it's deceiving because of the hard shell. You don't have anyone leaning back into you, and the cutout at the bottom provides extra legroom. JL has electronic controls while AA has manual controls. It takes a while to figure out JL's seat controls, but once you do, it's pretty easy to get into a comfortable position. The seat does go flat, but is still on an incline - pretty comfortable sleeping though. Back massage function works well on JL, and is much better than the balky lumbar function on the AA seat.

Food
Advantage JL
JL's food is geared towards the Japanese palate, but is still better than AA's catering, in IMO. AA's Japanese meal is actually pretty good, but not as good as JL's. JL meal service is extremely slow, though, which can be an issue if you want to eat and get to sleep quickly. Found that quantities on JL were better, as were the in-flight snacks and breakfast service on the Eastbound legs. JL has begun to upgrade it's meal service further, starting on the ORD flights. AA does have the advantage of warm nuts vs. JL's pre-pacakged snack mix.

Service
Advantage JL
JL is still geared more towards the Japanese traveler, so English isn't always fluent, but more than enough to be understood. JL's best crews are probably no better than AA's best, but their worst are a lot better than AA's worst. JL's cabin crews are hard-working and attentive the entire flight - and you can ring the call button for anything without fear of being reprimanded.

Cabin Ambience
Advantage JL
Perhaps it is unfair to compare the upper deck of a 747 on JL vs the large biz cabin of an AA 777, but JL's ambience wins big over AA. It is just a much more relaxing and peaceful experience. No clattering of dishes, no light constantly seeping out from behind curtains, no carts constantly running into your seat, no loud FAs...JL by a mile. For me, this was the biggest difference between AA and JL. Many fewer in-flight announcements on JL, and our experience is that seat belt sign isn't constantly going on and off...

IFE
Tie
Neither are very good. JL has a better screen, but both systems are outdated and limited compared to competing carriers. JL has the advantage of some games, but a lot of the music is catered towards Japanese tastes, and the movie selection is extremely limited.

Lounges
Advantage AA
Frankly, JL has a long way to go in terms of lounges. They are updating/renovating their lounges at Narita, but we didn't get to see them. JL's Sakura lounges in Chicago, Narita and Shanghai were nothing to write home about - free drinks and limited snacks, but that's about it. AA's new Admiral's Club @ Narita is terrific - spacious, light-filled, great showers, etc.

Amenity Kit
Advantage AA
JL doesn't give out an amenity kit beyond providing cabin slippers and cardigans on request. They did have a basket of things like toothbrushes, eye masks, etc on the NRT-LAX leg, but AA's kit with the Temple Spa products is much better.

Baggage
Advantage JL
JL tags priority bags for biz and first, and our experience is that they do really come out first.

Overall
Advantage JL
For the better seat and service, and much better cabin ambience, JL is the winner. For a route like ORD-NRT, it's a no-brainer. A little bit of a harder decision on ORD-NRT-PVG vs ORD-PVG non-stop...