As stated by others, I don't think you are going to get free upgrades on your TPAC flights so I suggest looking for value elsewhere.

Some considerations...
JAL frequent flyer program makes it somewhat easy to maintain oneworld sapphire status indefinitely, or so I've heard (JAL Global Club), if you can make status once. That might be a consideration. I have no background in JL's program, however it may be worth researching
Do you think flying around Japan for leisure on some weekends would be enjoyable? Flying around Japan with JL on AA miles is very fun. The redemption rates are good, JL domestic network & award availability is great, it's also just a pleasure to fly on JL domestically. I don't know how JL/UA/NH's program compares for domestic Japan travel. Anecdotally I think UA/NH is worse than AA/JL award-wise domestically. Could be valuable to go with a program whose miles will give you the most value.