There were plenty of people hanging around Harajuku on a Sunday afternoon when I went in February
It was a freezing cold, windy day and there were still plenty of cosplayers and people in alternative dress there posing for photos. If you're going there then Yoyogi Park and Meiji-jingu Shrine are beautiful and worth a look; interesting contrast to the crazy bustle of people on and across the bridge.
I found Shibuya pretty cool - it's what I pictured when I thought of Tokyo before going there. Lots of big buildings, that crosswalk with huge crowds of people, giant screens on the sides of buildings, bright lights everywhere. If you're into doujinshi then you'll love Mandarake bookstore... I spent ages in there
Kiyomizu was my favourite temple in Kyoto - there's a lot to see, including a really beautiful old cemetery off to one side. Gion was interesting too ,although I had a hard time finding a geisha to take a photo of, they don't seem to like it much. Not surprising I guess.
If you get bored of Kyoto then hop on a train to Osaka and go to the aquarium - it's GIGANTIC.