[godwine]

Hello there,

Shikoku and Kyushu's climate is not too different from that of the rest of Honshu. Kyushu maybe slightly more humid.

I counted 16 days, so with a 6 weeks trip, I think you have plenty of time to visit all the places you wanted to. Kyushu and Shikoku is nothing more than a brief stop, there aren't much to see, except for the great tunnel and the brdiges that connects the island (if you are a railway fan).

Then on your way back, you have the option to stop by Miyajima, Hiroshima, Himeji and then the usual Osaka and stuff, so I would recommend hitting up on those places as well.

Go have a look at Japan-Guide.com, they have very detail description of each places and what to see