Funnily enough, one of the companies that don't yet have tap-to-pay is... JR.
Each JR company also have their own website, and their own "network pass", making it quite cumbersome to book online tickets (e.g. needing to book each segment separately if they're on different companies' routes).
The Swiss system also has different companies, but everything can be booked on the SBB website/app.
I find Swiss system to be very convenient. My recent visit to the country was smooth thanks to the SBB app. It works not just for rail but also for bus, trams, and ferry. I think even some cable cars are covered. Plus there it can provide discounts or free visits to selected museums.