Mary, yes, Nara was my only day trip from Kyoto. Like I mentioned, I wanted to go to Osaka for a day too and had it in my itinerary, but I try (doesn't always work) to travel without pressuring myself to go here or there or do this or that. The night before I just felt like I'd been walking so much and had already been traveling around a lot (first Tokyo, then Hiroshima, and now Kyoto) that it would be better to just take a "chill" day in Kyoto and just wander around without any specific objective. I still ended up walking 25k+ steps the next day though haha. You'll do a lot of walking in Kyoto for sure.
I also would have liked to make a day trip to Uji from Kyoto. I've actually heard this can be combined with Nara or Osaka (I can't remember which one). But again, I try not to cram so many things into a day.
So, for me 7 nights felt just right. It was enough to hit the highlights of Kyoto without rushing from place to place and cramming my days full from sunrise to sunset. I typically only hit 2 temples/shrines per day. One in the morning, one in the afternoon. Some people like to cram in more. The thing is, temples are usually only open 9-5. I didn't want to rush from place to place. I like to stop and wander, take pictures, have lunch, etc.
Also, 2 of those days were going to be for day trips (although I only did 1). And the first day was really pretty much wasted because I stopped in Himeji on the way there and spent most of the day there so when I arrived in Kyoto it was already late afternoon.
I still didn't get to see everything in Kyoto either. I wanted to go see the Golden Temple and was going to combine it with my Arashiyama day, but I ended up spending more time in Arashiyama than planned (it was a beautiful day, the cherry blossoms were blooming, the monkey park was fun, the area along the river was lively). And like I mentioned getting around Kyoto takes more time than other places (I had to taxi to Arashiyama which was like a 30 minute drive if I remember and taxiing from Arashiyama to the Golden Temple would have taken another 30 with traffic, etc). so I just decided to spend the rest of the day in Arashiyama.
So, it really depends on the type of traveler you are and what you want to see. I know a lot of people do Kyoto in less time.
Yes, transportation is usually super easy. Typically in Europe I always reserve high speed trains in advance which can sometimes make you feel "locked-in" to a specific schedule. In Japan, I just went to the station the day of and bought Shinkansen tickets for the next train usually departing within the same hour (only exception to this might be during be holidays like Golden Week which is happening now). Something to keep in mind though, is many of the machines I saw (at least in Tokyo) for Shinkansen tickets said that if you pay by card you need a PIN code. Something us US travelers don't typically have with our cards. I didn't put it to the test, I just withdrew cash from an ATM at the station to buy my tickets.
Buses were pretty easy too. Get on from the back and tap you IC card, get off at the front and tap your IC card again. Only problem with the busses is depending on the city and route, they can be PACKED. Good thing is the drivers are patient and no one will rush you to get off.
Metros were also easy with IC card. I do wish I could have loaded my IC card on my phone to tap with the phone instead of card. It was annoying constantly having to dig out my card to exit the subway. (iPhone users can do this, us Android users can't). I will say the bigger stations (I'm looking at you Shinjuku) can be a bit difficult finding the exit you want. They are huge!
Taxis are easy and honest. They open the door automatically for you (no need to touch). All the ones I took accepted cards. Limited English though. Just show the driver your phone with Google Maps and the name or address where you want to go in Japanese.