1. If we had 2 weeks to spend, what should the break up be for these 3 places?It depends on your personal preferences! History, cities, beaches, shopping, .... What is more important to you?
For example:
5 days Okinawa
5 days Kyoto
4 days Osaka
How/where can I find cheapish accommodation that is smoke-free?On the internet. There are lots of reservation websites. Among them, the following offers good rates and an option to show only non-smoking rooms:
http://travel.rakuten.co.jp/en/3. How easy is it to get around Okinawa island without much knowledge of Japanese? and no car?Outside Naha it is challenging and inconvenient. The bus system is complicated and not easy to use even for Japanese people.
We have Australian driver's licences but not the international one (did not get it prior to leaving home). So is there no chance we can hire a rental car?No, I am afraid you cannot drive without an international driving license. And I think it is not possible to get one from outside your home country.
6. What will the weather be like in late Oct in Okinawa and late Oct-early Nov for Osaka/Kyoto? Will it rain much?Okinawa:
26 degrees average daytime high
21 degrees average nighttime low
57% sunny days
Kyoto/Osaka:
20 degrees average daytime high
12 degrees average nighttime low
65% sunny days
Is it better to stay near the main JR station in Osaka, or in town?In Osaka, the main JR stations are pretty much in town.
What about Kyoto?Downtown Kyoto has more and more attractive dining opportunities than the Kyoto Station area. I personally prefer to stay downtown (walking distance to Shijo-Kawaramachi).
Do we need to bring our our snorkeling equipment for Okinawa? (since we are not going in the summer time).I think you can rent it relatively easily.
Will USJ be crowded in October?Only on weekends and the national holiday (October 8).
How easy or hard is it to get a photo of a geisha/geiko in Gion?You need some luck to find a fake geisha in the Gion area (I found more of them in the Higashiyama/Kiyomizudera area). And it is neither easily possible nor recommended to take pictures with a real geisha. They usually hurry from the taxi into a tea house and most of them will probably be bothered by photo taking tourists.
Which is more worth going to: Ocean expo park in Okinawa, or Osaka Aquarium?Both are outstanding aquaria. But the one in Okinawa beats the one in Osaka, in my opinion (except for the horrible cafeteria food).