In case anyone misses the trend, the answer is train, train train. I lived in Tokyo 5 years and went to Osaka at least monthly and in all that time I may have taken the plane once. Getting to Haneda is a hassle from the city and the planes can be crowded (and expensive). There are several different Shinkansen trains and if you are into the small details try to get on one of the newer ones. They have different names (Nozomi, Hikari, etc) and I don't remember what the name of the fastest one is (I think it is the 700 series). On the way to Kyoto sit on the right side just in case Fuji-san is visible. Rare, but why take the chance of missing that spectacular sight. I do recommend spending the extra for the Green Car (first class) and unless you like smoke be sure to get non-smoking. Generally the obento boxes on the train are good, or there are tons of good obento shops in Tokyo station to get something before you board the train.

When in Kyoto you might try staying at the Three Sisters Inn (Okazaki, Sakyo-ku, Kyoto 606-8321. Phone (075) 761-6336 (reservations 8 am to 11 pm); international 81-75 761-6336). It is a western friendly traditional style inn.

One of the best holidays of our life was the 3 days we spent in Kyoto at the end of our 5 year stint in Japan. Kyoto is a very warm and magical city.
Gambatte kudasai (good luck).