JavaFX can call any Java APIs, so you can call JOGL directly from it if you want.
To make it easier to more quickly develop 3D programs, though, you need an abstraction layer. I have been talking with the tech lead of JavaFX, Chris Oliver, for several months about incorporating 3D. My first attempt at a higher-level abstraction layer is called the Minimal Scene Graph (“MSG”) and is checked in to the joglutils project on java.net under net.java.joglutils.msg. As the Javadoc describes, this is a small, lightweight scene graph which is designed for extensibility. The key thing many of the scene graphs out there today are missing is support for extensibility: the ability to add new types of nodes, new rendering effects, and new actions that can apply to the scene graph. MSG borrows many of the core ideas from SGI’s Open Inventor library from the mid-90s and I believe solves these problems. It should be portable on to other rendering libraries than OpenGL, and divides up the rendering state in such a way that the current functionality it supports isn’t hardwired into the scene graph. As one data point, Chris Campbell from the Java 2D team was able to add new nodes to MSG for the Iris demo we did at JavaOne (depth test control and shader support) very quickly.