I think most of the confusing experience comes from the way that Japanese limited express paper tickets used to work. If you rode a limited express (like Shinkansen or Narita Express), you'd have to buy two tickets: the basic fare ticket and the express surcharge ticket. The basic fare ticket would also cover your non-express connections, so this was quite convenient in Japan's complex transit system.
Japan still has that system in place, but the basic fare is usually replaced by your IC transit card or integrated into an eTicket (which contains both basic fare + express surcharge and is tied into your IC card).
So if you buy a ticket to NEX on the Ekinet app you'll be offered a ticketless option, but you probably wouldn't know that means you still need to tap your Suica in order to pay the basic fare.
Shinkansen trains are generally using eTickets, which would be even more confusing for visitors, but many visitors are using JR Pass which is completely outside the fare systems (but does need reserved seats).
Most of this complexity is inherent complexity, not accidental complexity that comes from bad software. The main issues I've seen with the software in question are: Lack of English version (Ekinet), Complex registration flow (SmartEX) and flaky authentication (Ekinet). This is not a great UX, but the apps don't feel worse than train operator apps in other countries. These are not tech companies.
Japan still has that system in place, but the basic fare is usually replaced by your IC transit card or integrated into an eTicket (which contains both basic fare + express surcharge and is tied into your IC card).
So if you buy a ticket to NEX on the Ekinet app you'll be offered a ticketless option, but you probably wouldn't know that means you still need to tap your Suica in order to pay the basic fare.
Shinkansen trains are generally using eTickets, which would be even more confusing for visitors, but many visitors are using JR Pass which is completely outside the fare systems (but does need reserved seats).
Most of this complexity is inherent complexity, not accidental complexity that comes from bad software. The main issues I've seen with the software in question are: Lack of English version (Ekinet), Complex registration flow (SmartEX) and flaky authentication (Ekinet). This is not a great UX, but the apps don't feel worse than train operator apps in other countries. These are not tech companies.