In many applications it may be necessary to use the UP and DOWN arrow keys for other purposes than navigating to the next focusable control. However, avoiding focus traversal is – as far as I can tell – not trivial to achieve.

Adding an EventHandler to consume the UP and DOWN key strokes does not help, since the focus traversal occurs before a custom key event handler is invoked.

Several developers have come accross this problem, and some have solved it by using an EventFilter to fool JavaFX into thinking that UP strokes are SHIFT+UP strokes and vice versa. One such example is documented here:
http://stackoverflow.com/questions/19625218/javafx-scrolling-vs-focus-traversal-with-arrow-keys

Although this approach may work, I consider it very elaborate and prone to future errors as JavaFX changes over time.

I suggest adding a feature to allow disabling of certain focus navigation keys per control, so that I can – for instance – change the selected element in a popup list when the user hits DOWN in a TextField of mine.