We deprecated the builders in FX 8, and froze the definition and implementation to match FX 2.2, primarily due to the fact that the way we generate the builders means that we cannot maintain binary compatibility if the class hierarchy of the core API evolves (e.g., if a method moves from a subclass to a superclass).The stated intention at that time was to remove these from jfxrt.jar in a future major release of Java (e.g., JDK 9) and provide them as a separate jar that could ship with an application, such as scene builder, that needs it. See RT-30520 for information on this.
The builders present a problem with JDK 9 because the modular JRE does not allow classes from a given package to come from multiple modules. When we modularize JavaFX we will run into this limitation. We will need to fix this problem in JDK 9.