As I have already mentioned in RT-16569 it is quite difficult to create a large scene graph or layout in code.
The reason for this is that the current API is just not flexible enough although that could be easily changed.
One severe problem is that you cannot reasonably set the layout constraints when adding nodes to a layout
pane like GridPane. But this could be easily fixed by modifying the static utility methods like setConstraints
so that instead of returning a void result they always return the node that they manipulate. This little change
would not break any existing API but would make it possible to define a layout in a simple way like this:

Pane pane = StackPaneBuilder.create().id("rootPane").children(
GridPaneBuilder.create().id("innerPane").hgap(10).vgap(10).columnConstraints(
ColumnConstraintsBuilder.create().build(),
ColumnConstraintsBuilder.create().hgrow(Priority.ALWAYS).build()
).children(
GridPane.setConstraints(LabelBuilder.create().text("First Name:").minWidth(100).build(), 0, 0),
GridPane.setConstraints(TextFieldBuilder.create().id("firstNameField").minWidth(200).prefColumnCount(30).build(), 1, 0),
GridPane.setConstraints(LabelBuilder.create().text("Last Name:").minWidth(100).build(), 0, 1),
GridPane.setConstraints(TextFieldBuilder.create().id("lastNameField").minWidth(200).prefColumnCount(30).build(), 1, 1),
GridPane.setConstraints(ButtonBuilder.create().text("Enter").onAction(handleButtonAction).build(), 1, 2),
GridPane.setConstraints(LabelBuilder.create().id("messageLabel")/*.styleClass("my-label")*/.text("messages go here").build(), 0, 3, 2, 1)
).build()
).build();

This is as compact as the corresponding FXML definition but has the advantage that it is type safe
and can also be easily refactored if needed. This scheme should be applied to all static utility methods
which manipulate a node in a similar way as the setConstraints method does.