I have 3 days to visit kyoto and osaka. I will start by tokyo. Please advice how to start and where to visit?

Question:

Answer:

You give no info about your interests, so it's rather hard to give concrete ideas.
There is so much to see, but a few places to see in Tokyo are:
Harajuku/Meiji Shrine on a Sunday to see the bizarre fashions
Senso-ji Temple in Asakusa - one of the famous temples every tourist goes to see
Odaiba at night for a real trip - try the ferris wheel and don't miss the Statue of Liberty and Venus Fort
See Love Hotel Hill in Dogenzaka near Shibuya Stn. at night for something uniquely Japanese
Tsukiji Fish Market at the crack of dawn.
Akihabara for the electronics.
Shinjuku and Shibuya at night for the endless lights and neon.
Ginza for the overpriced shopping.
Yasukuni for a real experience of NIhonjinron.
Tokyo Metropolitan Gov't Building in Shinjuku (better view from the top than the Tokyo Tower, and
all free!)
Roppongi for the ex-pat environment

For the Kansai area, Kyoto has numerous temples and shrines, Kiyomizu and Kinkakuji are some of the most famous. You should see http://www.jnto.go.jp for more info, and be sure to stop off at the tourist info office just across from Kyoto Station for lots of maps and info.
Since time is short, I'd say skip Osaka entirely - there is little there to see that you won't see more of in Tokyo. Instead be sure to go to Nara to see Todaiji and the Great Buddha; it is like the Taj Mahal of Japan.
If you plan to go by train, look into a JR Rail Pass - it can save a ton of money. There is more info
at http://www.japanrailpass.net