Your question has four questions bunched up, so just to break down and give you my thoughts.

1. You are flying JAL economy class and are looking for a “good” mileage program to credit the miles.
->If you only fly once a year or less, why limit yourself to Oneworld or the JAL direct flight?
I would suggest you look for something cheaper besides this direct flight. Or fly out of JFK/EWR where you have cheaper JAL, AA, ANA and UA. Or connect to the cheapest (Delta) via MSP/DTW.

2. Your ave potential plan to fly JAL again in the future, in economy class, and aspire to upgrade this future flight to business class using miles.
-> If your goal is to aspire to fly in business class, then JAL isn't the way to go. Award space (upgrade space) in business class rarely opens up, so you would need to book your ticket and upgrade it almost a year before you fly.
I would suggest you just keep looking out at the mileage run deals thread for a cheap business class deal to Japan from the US, and straight up buy a cash ticket. Alternatively, save up the miles and book an award ticket in business class straight up.
If you will likely only end up in economy on an expensive ticket (the upgradeable fares are expensive) , then JAL isn't the way to go. UNLESS, you are in a situation where you MUST take the direct flight and dont mind paying more for it.

3. You are looking for suggestions on earning more JAL miles towards the upgrade in no.2 above.
-> See the advice above.
Frankly, unless you are a frequent flyer with high miles/points earning frequency, you are better off going in another direction.

4. You are comparing JAL JMB with Cathay Asia miles and want to know which one is better for your needs.
-> If you are not a frequent flyer, then just go for the cheapest ticket and dont think too much about saving miles.
You will take years to have enough points/miles to redeem for a flight, and by then, finding a convenient date with the award space (or upgrade space) will be another heartbreaking challenge.