Interesting. We really enjoyed Tokyo, but spent most of our time there in smaller, out of the way areas. Absolutely loved it.
Though my favorite memories are from a super tiny seaside town (no public transport, ended up there because we misread the map) in the middle of nowhere.
If there's specific things you want to do that happen to be in Kyoto, I agree. I just think (somewhat from personal experience) that going to Kyoto because that's what you should do on a Japan trip is a bad idea.