Avoiding crowded trains is easy once you get the hold of it and as long as you're not in a hurry.
I have seen videos of station staff in Japanese tran stations helping and pushing people onto trains that are very full.Long story short, there aren't any pushers any more. I suppose they keep running 4-decade-old videos just to fascinate people who haven't seen real Japan.
Professional pushers mostly existed on the Yamanote Line, but I commuted to school and work during the most crowded era of the 1970s-80s, including the 4 years of using the Yamanote Line, and never encountered them.
Back in the days, however, I was indeed often pushed by commuters who wanted to board that specific train. I could've avoided that too, but I was always the slow person late for school/work and couldn't risk waiting for another train. But ever since I quit being a company employee to be given the choice to ride slower trains or less convenient trains, I've never experienced pushing/squeezing, even in central Tokyo. In all the months of being pregnant in the early 90s and onward, I always had the choice to ride trains where I was hardly pressed, and a lot of times I had the choice to sit which I still do.
Anyone is also free to obtain a "Helpmark" tag from a Metro station. It would help you be noticed by others so that they would surrender their seats for you.
https://translation2.j-server.com/LUCAIFUKUS/ns/tl.cgi/https://www.fuk...There are also priority seats on trains.
https://www.mlit.go.jp/hakusyo/transport/heisei10/index131/c6.htmlI myself use the tag and seats when my knee starts hurting again. And I'm a grey-haired elderly anyway.
I should also add that I ALWAYS have the choice to sit on suburban trains I use here in Greater Tokyo where I live with family who commutes to central Tokyo on a daily basis. The trick is to wait for a slower train that makes more stops.
I also agree with the other poster about choosing segments. At big stations, avoid staying near the stairs of the platform, and you're likely to find fewer people. Or best, you can watch one train coming in to see which wagons are less crowded. Then you can move to that segment and board the next train.
If I travel to the countryside, of course it's easy to get a seat in many of the less crowded trains, unless it's a special amenity train for tourists.
You can, of course, try the trains and give up for a taxi if you feel the trains are too stressful. Another option is to hire a local guide. A goodwill guide would cost you less/none. Local residents would know better about how to avoid the regular crowd.
You can also try to choose a hotel at the tip Tokyo rather than the center of it.
So, there are numerous ways to avoid crowds. I hope you and your wife have a pleasant stay here in Japan!