Thank you everyone for the fantastic advice!
NagaBaba: Thanks for the suggestion about local food/small hotels
I definitely prefer that approach, as I think it gives us a much more authentic experience. We'll actually be staying in Osaka for a good part of our trip, as a friend of ours is teaching english there, and has offered to put us up. I'm particularly looking forward to checking out Osaka Castle!
Briac & Guillaume: Thanks for the links! I'll check them out right now.
Robin: Thanks for the advice on staying at a Onsen-Ryokan. My wife and I were talking about the trip the other night, and we both really would like to check out something like that.
JJF: The lack of proximity to Hombu isn't a huge problem - we lived in Toronto for several years, so we're used to taking transit everywhere (though I imagine the system in Tokyo is just a bit more complicated...and crowded
). I'll definitely check out Minato-san's ryokan!