[MMM]

Depending on what time you land, immigration in Osaska (Kansai Intl Airport) is only 15-45 minutes.

I agree, spend at least a night (or 3) in Tokyo before heading to Kyoto and Osaka. But be prepared for the country to mostly shut down from 12.31 to 1.3.

And there is lots of great stuff to see in Tokyo, Osaka and Kyoto, but without having the foggiest idea what you are into, I am not even going to venture a guess. All of these cities literally have thousands of websites dedicated to describing what they offer for tourists (though you are going at a kind of crummy time). Ask about specific places, and I bet you'll get some educated responses.