If your plans only involve Kyoto and Tokyo, I don't think that a car offers much advantage in terms of flexibility of schedule - Trains between the two cities depart every five minutes or so, and take around two and a quarter hours. Making the same trip by car means having the flexibility to make the journey door-to-door but it will take several hours longer than the train. Within each city there are well developed transportation networks and lots of taxis.

Of course, there are folks who just love to drive, and if that's you then I won't try to dissuade you. Someone mentioned videos on YouTube. There are lots, but here's one of a couple who rented for five days, as you appear to be considering. They took a route through Kanazawa to get to Osaka. I would consider something like that to be a better use of a car than just going straight from Tokyo to Kyoto or Osaka, but to be honest, in both cases the routes are well served by high speed rail. Cars really come into their own when you go off the beaten track IMHO. But again, if you really like to drive then have at it.

Edit - Link to the video that I mentioned: