@edvin I haven't used this, but there was an enhancement to subcontrollers added to javafx 2.2 that lets you inject a root and a subcontroller into another controller. The mechanism that does this is an fx:define / fx:include pair which does not add the fx:include into the scene graph.
http://docs.oracle.com/javafx/2/fxml_get_started/whats_new2.htm