What you want to eat in the morning at Kyoto? The breakfast in your hotel, morning service at a nice cafe, morning ra-men, etc, etc.
There are too many choices in your Kyoto morning. I tried a special breakfast experience at Nijo-jo castle. Nijo-jo castle is a world heritage. The restaurant for this special breakfast is in the closed area we cannot go there usually, the area is Seiryu-en garden. This place is made for special guest like Lady Diana and Tom Cruise. At there only 40 breakfasts are served for the 40 guests in one day. The menu are typical Japanese dishes, Yuba Gayu plates.
We can eat them with beautiful Japanese garden. I think this is one of the best breakfast in Kyoto. You can make a reservation and eat it in June, July and August.