FXyz VS afterburner.fx

"and then a 3D line from there to the 3D sphere. " No, this line segment is also a 2D line. Actually its two lines of different colors, thickness and transparency which gives the illusion of 3D shading. I have a manager which reacts to any camera position/rotation changes by computing a transform of the 3D position of the sphere to a 2D point. The line segment's start x and y are bound to that 2D point. An example of how to do that same dynamic transform but with labels is in FXyz3d: https://github.com/FXyz/FXyz/blob/master/FXyz-Samples/src/main/java/org/fxyz3d/samples/utilities/FloatingLabels.java

The CAD models are slightly simplified versions of our machining models and exported as OBJ. They are more complex and produce more artifacts than hand-crafted models, but with instance sharing it's no issue to display hundreds of actuators simultaneously. Most of the models are 1-10MB, but the Hexapod chassis at the end is an unmodified export with ~150MB. The models are loaded using the OBJ loader bundled with FXyz.

You could handle the presentation aspects with a combination of FXML and controllers etc., or you could code the UI entirely in Java code using a kind of builder pattern described in the PragmaticCoding article I linked above. Another alternative is to use a framework like Afterburner.fx which uses it's own "convention over configuration" approach to building and structuring your presentation code.

The complex views are all built in FXML + CSS, but some of the simple views like charts are created programmatically. Different parts of the UI communicate via injected state using afterburner.fx for DI. We haven't run into any performance issues with FXML.