We had a 5 day trip from Tokyo to Kyoto, booked through japanican.com. A very smooth operation in all regards - the Bullet train both ways and 4 nights in a twin room at the Hokke Club. A great location just out of the northern entrance of the station - right across from the bus area, The hotel is almost next door to the Kyoto Dome.
The twin rooms are very comfortable and seem a lot bigger than the double rooms. The front desk staff are very friendly - high levels of staffing means you'll never have to wait for anything.
A great base for exploring Kyoto by foot - in the five days we caught only one train and one bus and manged to see most of this amazing city's historic sights. The only slight drawback is that most of the better spots for nightlife are a 20-30 walk uptown; most of the restaurants in the station area are more for a quick meal than a night out.
The package tour with the 4 nights accommodation was not much more than the cost of a return trip from Tokyo to Kyoto. All up, great value