Not all temples are equally geared toward tourists. Some actively cater to tourist traffic (to the point of having parking lots for tour buses and running television commercials preparatory to the lucrative New Year season). Most temples are not tourist destinations, but are more comparable to a small neighborhood church. No temple will turn you away or make you feel unwelcome, but you need to be aware that they are not all equally interesting to the tourist. Also keep in mind that while the temples do welcome everyone, a large portion of the Japanese tourists are there for sincere religious purposes.
Personally, I have always enjoyed the non-touristy temples the most. They're not the most scenic or impressive, but they have the advantage of peace and quiet as there is seldom if ever anyone else around. But when visiting for such a short time it might be best to visit the more famous and spectacular temples. If you have time, though, please try to drop by one of the neighborhood non-touristy temples so you can experience the contrast (and get an idea what the vast majority of temples in Japan are like....the famous and touristy spots are a very small minority).