Advice needed on structuring large directory site (Page templ. vs CPT's)

Hi,
I have been asked by a client to work on a rather large directory site. I created a sitemap to give you a better idea of the dimensions: https://www.dropbox.com/s/guxidvq6wvurrv4/Sitemap%20%281%29.png?dl=0

My plan is it to create custom post Types for each of the categories. For example the bus tours would be a custom post type, with taxonomies for the prefecture and the city (city would be a sub-taxonomy of the prefecture). My question now is: How would I create each of the landing pages. For example the overview landing page for all bus tours and the overview landing page for all bustours in city x. My thought would be to create custom page templates for bus tour prefecture and bus tour city. However page templates feel somewhat disconnected to the custom post type. Is there a smarter way to create the “taxonomy” landing pages? They should still be editable by the user (I am planning to use a lot of Advanced Custom Fields here).
I hope you get my point and can help me out here ??

Thanks,
Daniel