[Enea84]

First of all, many thanks for your good advices.
I decided to drop Okayama and Kurashiki because I kind of felt it wouldn't worth it after all.

So here is the update:

Tokyo: 5 days to see the city
Daytrips from Tokyo to : Nikko, Kamakura, Hakone, Mount Fuji, Yokohama = 5 days

Kyoto: 3 days
Daytrips from Kyoto (using the train):
Nara, Osaka, Himeji
Kanazawa, Shirakawa, Takayama, (Kamikochi, if opened)
Miyajima, Hiroshima (not sure yet) = 9 days

All in all, that would make 3 weeks.
It seems pretty good to me now, what do you think?