Tokyo or Kyoto?

Personally I loved Kyoto more than Tokyo, I liked Osaka too. I stayed in Mimaru Kyoto chain of hotels because I had my parents traveling with me so three people. It does not have onsen though. But keep in mind onsen hotels are generally more expensive.

If you take Shinkansen to Kyoto and back, google which side to sit for view of Mt.Fuji.

Kyoto for historic Japan, Tokyo for modern Japan.
The two cities are anagrams of each other.

I think the decision is based on what you want to see. As mentioned above, Kyoto is traditional Japan, and Tokyo is modern Japan. My impression of Osaka is that it is also more modern Japan. If you decide to go outside Tokyo, I would maybe wander Tokyo on your arrival day, train to Kyoto for Friday/Saturday/part of Sunday, and then head back to Tokyo. It's a short train ride to Osaka from Kyoto, so you could work in some time there, too, if Osaka is important to you. But I would do Osaka as a trip from a Kyoto base -- I definitely would not change hotels to go to Osaka. It's a 30-40 min train ride from Kyoto station to Osaka Station (depending on which train you take). I'm not recommending Osaka -- just presenting it as an option. I personally would NOT go to Osaka with so little time to see Kyoto -- to me, Osaka felt a lot like Tokyo.

As noted above, Osaka is commuting distance from Tokyo. with your timeframe, I also would recommend only a visit from Kyoto, not an overnight. That is if you decide there is anything in Osaka that is a "must-see" for you. The Dontonbori area has great street food and is a "fun" area. That could be an outing from Kyoto in the late afternoon, early evening if important to you. Beyond that, Osaka is definitely city with a few tourist highlights - family area with Universal Studios and aquarium, castle which has been turned into a museum. (Better castles to visit in Japan in my opinion.)

Kyoto is renowned for its temples and shrines, Nijo Castle, Geisha areas, history, neighboring Arashiyama, on and on and on. You would have no trouble filling your time. If you indicate your interests, I'm sure people would recommend their favorite spots.

Tokyo is massive - you could also easily spend your time there. Some great museums, interesting temples and shrines, a couple easy outings to nature areas with fabulous temple complexes if that is your preference. Take a look at Nikko and Kamakura.

I have not stayed in hotels that fit your criteria.

You are right - there are too many choices! Think of this as a start and plan for a return visit!!!!

As mentioned, Kyoto and Tokyo are polar opposites of each other. In fact, if you choose Kyoto, there is no need to visit Osaka, because you don't have much time on the ground.

My biggest concern is that, again, time is very limited for you. Going to Kyoto is great, but you lose some time in transit.

When are you going? Foliage season is super duper busy in Kyoto and hotels will be pricey. I am going to Tokyo, Kyoto, and Kyushu in late Nov and early Dec, when foliage peaks. I have already booked some of my hotels. In Kyoto, there are MANY hotel choices, from traditional inns (called "ryokans") to ultra modern, luxurious options. Kyoto hotels are more reasonable in price compared to Tokyo.

Suppose you choose to stay in Tokyo, you can always make a day trip to Kamakura, which is a mini version of Kyoto. Also, I highly recommend an overnight ryokan stay in Hakone, for the full Japanese hotspring experience.

Tough decision, but I think you cannot go wrong with either choice. It really depends on your personal preference.

Seininya- Great idea to Google which side to sit to get view of Mt.Fuji, I didn't realize that was a possibility to see while traveling by train, thank you!

Kenko-I was thinking the same thing about the names!

Dave-I like the idea of doing Osaka as a day trip from Kyoto but as I'm learning, there is so much to see in Kyoto that my timeline is a bit crunched for all that, so I may not if it takes away time to see Kyoto.

ORDtraveler-I agree! I think I need to plan a return visit, and with more time!

Barkinpark-I am going in July enroute to Bangkok. Apparently, not the ideal time due to the heat and humidity (?) but it's the only time I have. I do like the idea of using Tokyo as a base and visiting other smaller, and closer, cities that are similar to Kyoto, at least do so gives me a taste of the areas. I don't want to loss time in transit. I like to travel by food so want to find local places that allow me to discover foods not found in the states.

In general, I like to soak in the character of a place by seeking out things that are less touristy in nature. I feel like it's like being in a candy store - can't have everything so gotta pick the main thing I really want.

Thank you all for great ideas!

With such a short trip flying in an out of Tokyo, I'd be inclined to leave Kyoto for another visit. I second ORDTraveler's suggestions of Kamakura and Nikko for something that feels a little more like Kyoto or "traditional" Japan as opposed to modern Tokyo. There are corners of Tokyo that feel that way too, but might be hard for a first time visitor to find on such a short trip.

Other possibilities to consider as day trips from Tokyo are Kawagoe and Hakone. Hakone is a little long for a day trip, but I've done it. There is a transit circuit that takes you on a loop through the area and includes a boat across a lake. If an onsen is really important to you - there are some in Hakone. I spent the last part of my day trip to Hakone at an onsen before catching the train back to Tokyo.

We were just in all the cities this past March. My answer would depend on your age. We’re in our late 60’s.
Tokyo is amazing. We spent 9 days there and loved it. So modern but also very traditional.
Osaka is a food scene and definitely for the younger crowd.
Kyoto is very traditional, wasn’t bombed during the war so no skyscrapers or neon, etc.
Hakone was boring for us, and Kawagoe was a nice day trip from Tokyo but I would skip it with such a short time period.

With so few days, and flying in and out of Tokyo, I would stay in Tokyo the whole time and possibly consider a day trip to Kanakura for more traditional sights nearer by than Kyoto. There are also traditional shrine sights in Tokyo such as ones near the Imperial Palace and in the Asakusa neighborhood. Alternatively, if you choose Kyoto, I would just do Kyoto and if possible see if you you fly in and/out of the Osaka airport.

Agree that with just 3 days, I'd suggest you skip the side trip to Kyoto, and stay in Tokyo - you could do a day trip out-and-back one day, but be careful not to overload your plans, you will probably arrive tired, and Tokyo can initially feel a bit overwhelming. Especially in the heat and humidity of July. It's understandable to try and squeeze in a lot in your limited time there, but don't expect too much of yourself. If this is your first trip to Asia, there's going to be a bit of culture shock initially.

Kyoto is the gem of Japan. It takes a minimum of 3 days to take in the best of its great sites.
I suggest planning a future trip to Kyoto that also includes Osaka, Himeji Castle and Nara. You would need 5-6 days to do that.
Tokyo is wonderful and you can see a lot of it in three days, but not all.

Come back to Japan and spend a couple of weeks and do all these places. Consider Nikko north of Tokyo for a day trip an Kamakura, near Tokyo for the giant Buddha.