JavaFX no longer has its own scripting language. You write the code in Java, but you get the JavaFX components, shapes, etc.
Nashorn is nothing like GWT. It is pure JavaScript, but with extensions to manipulate Java objects. It's meant for end-user programmability, kind of like VBScript in MS Office. You expose some Java objects and then run the user's script which manipulates them. The idea is that more users will be comfortable with JavaScript. They don't need to compile anything or know how to read javadoc.
In fact, you can write JavaFX programs in Nashorn. It's not as convenient as the JavaFX Script language used to be, but it could be pretty close if someone worked at imitating the old builder syntax with nested JS objects.
In general, there are too many custom languages. Look at Processing (
http://processing.org/). The graphics are great. But having to learn yet another small language, designed by well-meaning amateurs, is annoying. They didn't think a Java API would work for their user base, and I can agree with that. If they had then what we have now, they could just expose an API to JavaScript (just like the DOM API is exposed in a browser). JavaScript may not be wonderful, but it isn't terrible either, and the investment of mastering its quirks pays off elsewhere. So, if your project needs end-user scripting, check out Nashorn.
Cheers,
Cay