Unless you're talking about mainland Chinese airlines, there's no comparison between Economy and Premium Economy. It's pretty much always a lot better. I haven't been on the mainland Chinese carriers in a while but their idea of Premium Economy at least used to be extra legroom only (like AA MCE, or UA Economy Plus).

I am not a huge fan of JL's PE (though I know you're not weighing that option), as they serve economy food and drinks, most other airlines elevate those a bit for PY.

As others have noted, JL's IFE is God awful but if you're going to watch some Japanese movies then you may not notice.

I think this is an easy question though, any airline that isn't CZ, MU, or CA, the PY will be better than Y on JL.

There's also one other thing that I absolutely despise on JL in Y... the FA's will force you to keep your seat upright during meal services. Note they serve the 'breakfast' arrival meal a full 2 hours before arrival, waking up the entire cabin needlessly early. If you're needing some sleep and it takes you a bit of time to get into it, JL is pretty annoying in that regard.