If you are developing a UI framework for JavaFX, then please make it a habit to always split your custom controls into a control class and a skin class. Coming from Swing myself this was not obvious to me right away. Swing also uses an MVC concept and delegates the actual component rendering to a UI delegate, but people extending Swing mostly subclassed one of its controls and added extensions / modifications to the subclass. Only very few frameworks actually worked with the UI delegates (e.g. MacWidgets).
I have the luxury of being able to compare the implementation of the same product / control once done in Swing and once done in JavaFX and I noticed that the JavaFX implementation is so much cleaner, largely because of the splitting in controls and skins (next in row: CSS styling and property binding). In Swing I was exposing a lot of things to the framework user that I personally considered “implementation detail” but that became public API nevertheless. The JavaFX architecture makes it much more obvious where the framework developer draws the line between public and internal API.
The control class stores the state of the control and provides methods to interact with it. State information can be: the data visualized by the control (e.g. the items in TableView), visual attributes (show this, hide that), factories (e.g. cell factories). Interaction can be: scroll to an item, show a given time, do this, do that. The control class is the contract between your framework code and the application using the framework. It should be well designed, clean, stable, and final.
This is the place to go nuts, the Wild West. The skin creates the visual representation of your control by composing already existing controls or by extending the very basic classes, such as Node or Region. Skins are often placed in separate packages with package names that imply that the API contained inside of them is not considered for public use. If somebody does use them then at their own risk because the framework developer (you) might decide to change them from release to release.