Shinkansen is comfortable than airline, no annoying inspection, almost no wait, and utilization is high enough. So technically it should be priced higher than airline, but I also feel it's weird that high CO2 emission airline is cheaper than lower emission train.
For whatever reason (probably just inertia), JR has been highly resistant to adopt dynamic pricing, so Shinkansen tickets costs the same regardless of whether you travel at absolute peak or when the trains are rattlingly empty. This is starting to crumble at the edges a little bit, and I expect advance-purchase fares to plunge if they ever do make the leap.
Yes it's one of the reason to choose airplane for individuals. Govt's regulation for train is an another reason why dynamic pricing aren't done well but it's changing. Currently train+hotel Dynamic Package is available as a cheaper option, but it's not for single day use.
Oh, neat, I recall a trial of that but didn't realize it was rolled out permanently. And apparently you can even book tickets online without jumping through insane hoops! Huzzah!
Yes, it’s competitive with airlines but it’s often more expensive. This makes sense as it’s nicer, but I think people looking at the system from overseas don’t realize this. That might also be due to how good the unlimited flat rate tourist passes are.
Besides renting/owning a car, the real cheap option for intercity travel is night buses.