It really depends what you're interested in, but given you want to do the Osamu Tezuka museum and Den Den town, I'm going to assume we have similar interests. I did Kyoto once, but didn't really think it was worth the travel from Tokyo (though I did only spend a day there).
We went to the kinkakuji and while it made for some nice photos, there wasn't much else there that we hadn't already seen before. Osaka, on the other hand, was way more up my alley. Plenty to do there, although don't expect Den Den Town to be as big/diverse as Akihabara. The Aquarium was great, too. I assume you want to see the whale shark? Can't comment on the museum as I haven't been myself.
I'm sure there are others here who can give you more info on Kyoto, but just do what you want to do, don't worry about doing it because you feel you have to