I've never been to Kyoto, but looknig quickly on google maps:
https://goo.gl/maps/SgnriwRthWYWtsv19
It's pretty hemmed in by mountains. Did hey have much choice other than to build up? From the centre to mountains is under 10km in almost any direction.
I'm not saying we haven't made poor decisions regarding transit, but it can be simplistic to compare ourselves to other cities. Pre-oil crash of 2014, I think Calgary had a really well used transit system that wasn't meant only for poor people.