Kyoto is massive and traveling here can be a hectic experience, especially if you are short on time. We came to Kyoto from Tokyo and spent only three days in the historical capital. These small tips took little preparation but made a huge difference in the overall experience.
Stay in a Ryokan or centrally located hotel (and book well in advance)
Ryokans are traditional Japanese Inns with a communal feel. Matts are rolled out at night to sleep and tucked away in the morning for space during the day. The minimal zen vibes of these inns provide a very traditional Japanese experience. Be sure to book well in advance as these can be costly and they book up fast. If you are not into sleeping on the floor (understandable), other hotels like Citadines still have minimal vibes with a comfortable bed without breaking the bank.
Rent a scooter or bike to get around
Kyoto is very spread out as one of the largest cities in Japan. The best sights are often clear across town and it can take 45 minutes just to get from one to the other by car. The subway system, while efficient, can require multiple train changes and stops in order to get around, not to mention you are below ground that whole time.
The best way to get around is by motorbike/scooter. We rented these for $70 USD a day: not cheap but considerably less than taxis. The subway is not particularly cheap so this wasn't too bad relatively speaking.
Rental 819 was a great company near the subway. Be sure to have your passport, international drivers license (something easily obtained from AAA for $25 in the US without an appointment), and regular driver's license. Contrary to what their website says, you do not need to speak Japanese. From there the world is your oyster!
If you are unable to rent a scooter for whatever reason, there are regular bike rentals all over the city. These are great options for some of the closer-together sights and can be a good work out. :)
Eat Clean Foods
There are some crazy looking food vendors all over Japan that can be tempting. From mochi, to crab on a stick, to soft serve ice cream...treats are everywhere! Traditional restaurants in Kyoto are mainly BBQ and soba noodle based. It is good to seek out some of the healthier places first so you don't resort to these.
Sushi is not as popular (or good) because it is not in close proximity to the ocean compared to Tokyo. Indulging in noodles and mochi every now and then is fine but keeping your diet clean will leave you with the energy to tackle all of Kyoto's sights.
Mumokuteki was my favorite vegan spot with beautiful steamed vegetables free of gross additives and oils. The restaurant had a wide array of macrobiotic and vegan options - I practically lived there. The brown rice was cooked with such care and perfection.
A huge downside to Kyoto are the crazy number of tourists...everywhere. Kyoto is worth visiting and dealing with the crowds but the earlier I went to the shrines and temples the better. Next time I visit I am going during the off season just to avoid it all. Set your alarm for, no joke, 6am and get moving.