We were lucky to hit Kyoto right at the peak cherry blossom season in April of 2011 (yes, just a few weeks after the devastating earthquake and tsunami rocked the East coast of Japan).
We spent four nights in Kyoto at the Hotel Granvia (located right in the train station). It was a fantastic hotel, and due to the devastation, rates were low as tourists were few and far between. Their loss, as the people, the town, and the cherry blossoms were amazing.