Update Nov 2020
This answer is now outdated.
As various more recent answers have pointed out, there are now a variety of additional different tools available for automatically generating FXML controller classes from FXML documents. Many of these are targeted as extensions, features or plugins to existing development tools, such as SceneBuilder, Idea, Eclipse or NetBeans.
I suggest that interested readers review both this answer and other answers to this question, then look at their individual use-case and toolset chain and choose the solution which is most appropriate for them from the available choices.
There is nothing I know that does exactly what you propose in your question.
Likely this answer will probably end up pretty outdated over time.
Alternate Technologies
JRuby achieves most of your outlined benefits using a slightly different approach - it uses jRuby's dynamic programming magic to automatically create Ruby class members from the FXML dynamically a runtime.
Tom Schindl wrote a tool which generates Java code from FXML. Of the approaches listed in this answer, Tom's tool seems closest to your question.
SceneBuilder Skeletons
A similar Java code generator from FXML is available in SceneBuilder View | Show Sample Controller Skeleton
feature, which is described in this blog post. When I use SceneBuilder, I use this feature all the time and try to keep my controllers really light so they are almost all auto generated code from the SceneBuilder skeleton feature.
It is slightly annoying though because it doesn't achieve a clean separation of generated code from hand written code, so you need to be careful when you do updates to the FXML and want to generate a new skeleton and copy and paste it over parts of your existing Controller (plus that is a slightly error prone manual operation that takes a little bit of developer time).
Source code for SceneBuilder is available if you want to see how it works.
Potential Build Tool Plugins
Such a code generation feature might make a worthwhile addition to some of the existing build tools in the JavaFX ecosystem, such as the JavaFX Maven plugin or JavaFX Gradle plugin (or a separate plugin in it's own right).
Future Development
I believe that Oracle are also working on a feature extension for FXML for a future JavaFX release (post Java 8) which compiles FXML directly to Java byte code (class files), bypassing the Java source code step. This kind of feature would probably achieve most of your outlined benefits.