It is true that in Japan there are many local stations that only arrive a few times a day, but I’ve found that this is generally for places that are very low traffic; ala middle of nowhere Fukushima countryside train. I’m usually more surpised the train system even goes there than I am surprised by the frequency. For pretty much anywhere you’d expect local trains to exist, they’re usually very good. Not trying to compare countries or anything (I’ve never been to Switzerland). Just describing my experience in Japan (not expert; only lived there ~6mo)
As I said, I’m not trying to compare or enter a discussion about what system is better, since I’ve never been to Switzerland. I like it when places have good trains, and it sounds like both places have that. So that’s good enough for me. I was just replying to give you a better idea of what it’s like in Japan.