Kata training in Japan, worth it? where to go?

[Wastelander]

On the mainland, you could also reach out to Joe Swift. His account on Facebook is Dojo TokyoMushinkan.

[Spartacus Maximus]

One must bear in mind that training in Japan or even Okinawa is no different than training anywhere else. It is not a matter of where but with whom. That is what makes the experience worthwhile.

With that said the best course of planning, as others have mentioned is to arrange it through connections and references. These are extremely important and perhaps essential. In many instances just showing up without an internal referral is a major blunder which will give a rude impression and cause for refusal or cold reception. 

Many traditionally minded sensei and Japanese people in general are weary of foreigners unless they have a clear signs of good faith and respectable intentions. Expect to be closely watched and scrutinized in the dojo and outside as well.

In recent years there has been much conflict, frustration and justified anger because of a few ill-behaved, uncouth and foul uncivilized behaviour from foreigners who seem to think they can abuse the kind and polite nature of Japanese society. Mistaking this for weakness always ends badly and those who behave like trash are treated like trash. 

The man to look up in Okinawa is Mister Miguel DaLuz. He has lived there for years, and is very well connected to all styles sensei. It is actually his job to help foreign karate students find a dojo. He also runs a great magazine covering karate, history and Okinawan culture published in French, English, Spanish and Japanese which he speaks flawlessly. A very interesting fellow to talk to.

The mainland is less familiar to me, but there are quite a few reputable places in and around Tokyo.