I just gave this some more thought:

Kyushu and all that would be very nice... but it may be best to send her to the places you've actually been to, since you can tell her about those with confidence. A lot of people visit the Kansai region on their first Japan trip - and not without reason. So perhaps it's not a bad idea to suggest Kyoto, Nara and one of your favourite rural spots for a bit of contrast.

As far as onsen go - I think Kurama is just great.

Oh... and from Yokohama, don't forget that Kamakura is right on your doorstep. That might be a great start to the relaxing holiday. No need to even move to another hotel...