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SceneBuilder 2 brings support of an empty FXML, but point is "empty" doesn't have the same meaning for the NB 8 "Empty FXML" wizard: for SB 2 empty means a file which has absolutely no content inside, which is new compared to SB 1.*. But of course attaching a controller and styling as done by the wizard isn't possible if you don't have at least one FXML element. There's another "message" SB 2 brings which is that AnchorPane isn't the only way (at start SB2 opens on an empty content and one can go with any container, AnchorPane is only one option). Basically is one uses an AnchorPane it's better be on purpose. As a conclusion I wonder if NB 8 wizard couldn't be renamed something like "Configured FXML": in addition to controller and styling setting the user could also select the class of the root element to choose among all containers of FX 8. And in addition may be the "Empty FXML" could be kept aside but simply to create a really empty file.
I think the command should be renamed from "New Empty FXML file" to "New FXML file". If you want an _empty_ FXML file, fire up Scene Builder. See Bug 241426 You have some good ideas. I'm not sure about adding a bunch of selectable FXML templates (including "empty") to the New FXML File Wizard. It might be good (?). New users might find it confusing, if that matters.