I have been there for two weeks last may. Just missed the cherry blossom time. But the heat was not that extreme yet. I found Myajima, Kamakura and Kanazawa to be some of the highlights. Especially Myajima, when most tourists are gone in the evening and you can have a serene walk on the beach, next to some of the most beautiful shrines and landscapes of the country.
I don't like big citys and apart from the arcades in Akihabara, some cute animal cafés and the big tower, Tokyo did not do much for me.
Kobe was a bit of a disappointment. The harbour is nice and the flower/herb-gardens above the city are beautiful. The meat is superb. But the city itself I found to be rather ugly.
Navigation can be tricky and many people don't speak english, including sevice personell in public transport stations. So I would recommend having a phone handy for translation (paired with a travel wlan, to have internet access wherever you go - also to pinpoint your location and find cool spots to check out).
Edit 1: I was 2 weeks and this was enough for me. I would like to come back one day. Perhaps in a few years.