If you have to spend four nights in Tokyo then I would spending a day and a half in Kyoto and dropping Nara from your itinerary.
Why are you staying at two different Kyoto hotels during your two nights there? That doesn't make a lot of sense. Are you going to leave your bags at the Ryokan, go to Nara, come back to the Ryokan to collect your bags, then go to the Hyatt?
The Hyatt is close to the station and right next to the Kyoto National Museum and Rengeoin Sanjusangendo. It would be much more convenient for you to stay there for two nights since you will be arriving and departing by train, and especially if you are also doing the day trip by train to Nara (which I don't recommend).