I get jet lag really bad. And I think kyoto takes more energy- more walking. So I would end in Kyoto.


But on the other hand, it depends on your interests. If you aren't going to do hardcore sightseeing in Kyoto, you could start with it. It is a major city but it feels more intimate than Tokyo, and it has had the most foreign tourists I've seen so far. Better introduction to Japan imo.

Another idea: do you plan to do another trip to Japan? Because I would probably choose Kyoto, Osaka and Hiroshima for this trip, and do Tokyo another time. I think you'll want more time than 3 days in both places. Osaka would be bright lights/big city, and a fun contrast to Kyoto.