I am jumping in as we will also be first-timers to Japan next July

I see plenty of nice hotels (SPG, HH, IC, Hyatt...) in Tokyo, Osaka, and some other big cities.
However, according to tripadvisor, it seems somehow difficult to find adequate lodging in "smaller" cities (i.e. Nara or Nikko, Hiroshima).

How to be sure to make the right choice at the right price (We are not on a budget trip)
Is it better to use Tokyo or Osaka as a "hub" and take the Shinkansen for day trips ?