Using the FXML would be the better option. Note that, the SceneBuilder - an UI builder app released by Oracle to design JavaFX screens produces an FXML...so, if you have an FXML, other developers can simply open it in the SceneBuilder and change the screen design in an easier way.
Also, many other modern UI toolkits follow the same pattern (ex.:Android).
SCJP 1.4, OCMJEA/SCEA 5.0.
subject: preferred way for working in JAVAFX ? JavaFX FXML application or simple JavaFX application ?