I noticed a lot of mention of how luggage can be a pain, especially on the subway & "rapid" (local?) trains. For two of us, we plan on doing entirely airplane carryon: Two small napsacks and two (overhead-compartment-friendly) rolling bags. Would this be considered "bulky"?
That's OK for two persons. I traveled solo with half that amount and never had problems.
If you are going to use
coin lockers to store your rolling bags while sightseeing (they are found at virtually every railway station and are very convenient), keep in mind that most common "small-size" coin lockers are sometimes a little bit smaller than the carry-on size. I had no problem with a semi-soft rolling bag, but I can imagine that a hard case may not fit into some.
Another thing I found out the hard way is that when you make separate reservations for consecutive nights at the same hotel via Expedia, Japanese tend to merge them into a single reservation. When you cancel one of the nights, this single reservation gets canceled and then you have a problem when you arrive. For me, the problem always meant an upgrade into a nicer (and available) room, but I suppose the luck can also turn the other way round.