Spring is the perfect season to go to Japan... Cherry blossoms, a few people, a lot of temples to visit!
Tokyo is perfect if you want to walk a lot. Especially during night you can see the Sensoji (Asakusa Kannon Temple) with wonderful artificial light. I like the five storied pagoda in nocturnal illumination!
Kyoto is the most famous city if you want to live ancient traditions (tea ceremony, geisha dances...) or if you want to visit beautiful buildings, like the Gold Pavilion, with a very nice garden reflecting the light of gold leaves from the roof of the temple.
In Osaka you can see the "Osaka Castle", one of the most famous defensive fortification of Japan, surrounded by a large garden when you can have a pick-nick or do some birds watching!
Don't lose the opportunity to go and see the Himeji flatland-mountain Japanese white castle complex! It was also registered as the first Japanese National Cultural Treasure by UNESCO.