fh2000 wrote:[...]which passport should we use: Taiwan or US? Or does it matter since Japan does not require visa from either country?
A few things come to mind (not to be taken as advice, just something to consider):
You already know that either PP will be basically OK, but does it matter into you in which PP the J immigration stamps are stamped?
I imagine that using the US PP might possibly mean less hassle (scrutiny, suspicion, etc.), but if you show a return ticket and, if asked about funds, show them credit cards, there should be no issue whatsoever being a Taiwanese visitor to Japan.
If the Taiwan entry and exit stamps are not in the US PP at the time you go to Japan the officer may assume you are coming directly from the US (see above: less hassle), unless you are in the line with all the other passengers coming directly from Taiwan - if I was on duty there I would then expect Taiwanese stamps in your passport. But if you, on questioning, explain that you have two passports, it should not be a problem.
If you go again in the future and use a different country's passport but with the same names, it might cause some raised eyebrows. If your names are written differently in the different passports, it will likely mean that they think you are different people. ;-)
But you might just go/call and ask the Japanese rep office in Taipei for advice!
As always, anything said or written about Japan in relation to foreigners should be qualified by ESID ("every situation is different") - in other words: nobody can answer your question with certainty.