Larger luggage and train travel are a bad combination, and not only in Japan. You'll have to negotiate stairs at times, and may have steps up/down getting on/off trains, all apart from where to keep your bags once aboard.
Consider an int'l carry-on suitcase and a travel-type backpack, e.g.,
https://www.nomatic.com/collections/travel-bags/products/nomatic-30l-travel-bag for each traveler. Bring minimalist ultra-light, packable clothing meant for backpacking, to reduce bulk and weight. For example, I have a rain jacket I only use for travel. It is completely waterproof, but has a single plastic main zipper, only two slash front pockets, compacts down to fit into a very small stuff sac, and weighs almost nothing. It was quite expensive, ironically, given that it has few features apart from being lightweight and packable, but that's typical of clothing meant for a specific application like that. It's not durable or fullly-featured enough for me to use it routinely, but it's ideal for travel. You can find similar characteristics in shirts, trousers, mid-layers, and underwear. Alternate between just two pair of shoes, one of which should be waterproof; you wear one pair on the plane and have just one pair to pack. Etc.