The downside is that it is sometimes hard to transfer between local train lines, since they do not share the same train stations.
As if that wasn't enough, then there are the buses. The benefit of buses is that there are many more bus stations than train stations. Everywhere I have been in Kyoto, I have never had to walk more than seven minutes to get to a bus station. There are four different bus companies in Kyoto. This can make it confusing because sometimes the bus stops are right next to each other and you don't know where to wait. To make matters worse, sometimes different companies have buses with the same number! When my mom visited me, she was waiting for Bus #5 and got on it when it arrived. However, it turned out to be a different company's Bus #5, and therefore it took her to a completely different place.
Finally, there are bikes. Unlike the other vehicles mentioned, bikes are not a form of public transportation. However, many people in Kyoto have bikes. I have seen everyone from six-year-old children to 90-year-old great-grandparents riding their bikes everywhere. In Kyoto University, people bike between classes that are less than ten minutes walking distance apart. People often go grocery shopping on their bikes and carry goods home in an attached front basket. In fact, some grocery stores have bigger bike parking lots than car parking lots. In bike parking lots, the bikes are stuffed so closely together that you can't even tell they are bikes. In fact, the first time I saw a bike parking lot, I thought it was a pile of junk metal!