Flights booked! Very spenny but my wife's a teacher and thats just the price you pay for that.
So we're thinking of doing 5 nights in Tokyo, 5 nights in Kyoto and 2 nights in Osaka, with one night back in Tokyo ready to fly home. We've decided against Hakone, and Hiroshima. I've been to Hiroshima, but the main draw there is Miyajima, which my wife isn't bothered about, and the peace park, again she's not too bothered, I've already been to both. Hakone looks lovely, but I've been and I don't recall being that enthused by it, and my wife isn't too bothered either. My wife has a lifetime dream of going to every Disneyland in the world (my worst nightmare), but marriage is about compromise, right? So I guess one day in Tokyo will be going to Disneyland.
As far as places to stay I've been looking at Ueno in Tokyo, it's right on the yamanote line and good links for airports. In Kyoto I've been looking at Gion, and for Osaka I've been looking at Namba