I’d say this very much depends on the project. JavaFX is awesome and there’s a guy who maintains a JFX game library here which you may be interested in: https://github.com/AlmasB/FXGL
I can’t give much insight on it since I generally build my own architecture when I use JFX, but it’s almost certainly a faster starting point. It does (IMO) seem a little more oriented towards “2D shooter / console” type of game.
JavaFX will help you lots if you have a GUI intensive case, especially if it’s intensive enough that you need/want to visually lay out your UI with a tool (search for “Gluon Scene Builder”). JavaFX does have 3D capabilities accessible, but I would recommend JME if you’re doing significant 3D stuff. So I guess the reason you may choose JFX for a 3D game over JME would be when you have a UI intensive case, and only need basic 3D graphics (i.e. game is more about content than graphics).
JME has the advantage in 3D capabilities and community/help. Lemur is a great little UI lib for JME, but if you need more complex UI components, you may need to build those yourself. I would say JFX has an advantage on learning curve (if 2D), documentation (on the UI side especially), and complex UI support. There is Java Swing out there still, but one of the big perks JFX has over Swing is css based custom styling (important for game UI) so I’d probably keep Swing off the evaluation list.