Where to visit in September

I am confused. Where to visit in Sept? 1) Kyoto-Nara-Osaka. 2) Tokyo. 3) Hokkaido if I only have 7 days to do it in Sept.

You don't have to be confused. It just depends on what you want to see and do during your stay in Japan.

If you are for history, pick option 1) and appreciate the beauty of Kyoto and Nara.

If you are for cities, pick 2) and if you are for nature, pick 3)

you can easily visit 1)Kyoto-Nara-Osaka. 2) Tokyo, and many more places in 7 days.

I wouldn't say one can visit a lots of places in 7 days but one can have a brief snapshop of Japan:
day 1: arrival in Tokyo
if landing early enough (before 4 pm) go to Kyoto by train from Narita (change to another train in Tokyo or Shinagawa)
day 2: Kyoto
day 3: Fushimi-Inari and Nara
day 4: Osaka
day 5: Kyoto-Tokyo
day 6: Tokyo
day 7: departure.
if you meant 7 days in Japan, not including arrival and departure then you can add 1 day in Tokyo and 1 in Kyoto.
you can stay in Kyoto or Osaka as the yare only 0 minutes apart by train.
ckeck this site for old threads on visiting Kyoto, Tokyo etc.

Thanks for the posts.
I would like to know if it is a good time to visit Hakodate and places around Sapporo in Sept. I am more towards natural...