My plans for Kyoto were to spend lots of times in the gardens and shrines. When we left Tokyo we left most of our clothes and luggage at hotel so we could travel light. Which at the time seemed sensible. Except when the only pair of shoes gets soaking wet. And your one pair of pants are drenched. My feet look like prunes having walked around for hours with wet socks and shoes. Thank goodness for moleskin and Bandaids.
But we did not let it deter us. We simply rearranged plans and saw things in the pouring rain. Some parts of that were good. For instance the rain made the moss gardens sparkle and the bamboo forest was even more dramatic in the rain. Today, the day the typhoon hit Kyoto we spent the time looking at the covered market and taking a cooking class we had signed up for. And the rain broke for 1/2 hour so we could walk in some back alleys.
Also so much of both Tokyo and Kyoto are underground so you can walk through a large part of the city through the train and subway connections which are filled with wonderful shops and eateries. It is quite and experience just to walk form one line to another. A different planet than the urine soaked subways of NYC. So we did not mind being underground out of the rain. But I would like to see Japan more clearly when my glasses are not fogged up!