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SceneBuilder works with lots of different IDEs and without an IDE at all.
I don't think matisse (?) did (though I never used it).
I think that's an advantage.
If you wished, you could file a request against the NetBeans project for them to co-bundle SceneBuilder.
The plan for NetBeans 8 (http://wiki.netbeans.org/EditorPlan80#JavaFX_2) has an item:
"Ongoing support of SceneBuilder interoperability plugin (?, ? days)"
I think the first question mark means no owner has been assigned the task and the second question mark means nobody knows how long it would take.
Yes, the independent design of SceneBuilder is certainly an advantage. In fact the integration has worked well so far. However, my original request is still valid for a newbie user.
For a mid/advanced user the 'tool-chain' approach has advantages. (Unix tool's style).
The independent tool/plugin approach also encourages other technologies (esp xml based) to be incorporated relatively easily. For e.g 3D designer or a domain specific tool .