We have developed the faces scaffold to be able to generate a simple jSF application without any deep layering, because that's the simpler way to have a Java EE application running. Since there are many architecture variarions including, but not limited to, the use of components frameworks, like Richfaces and the like, we think that the best approach to generate the ideal scaffold is creating another ScaffoldProvider as a Forge Plugin with your desirable architecture. We already have a few implementations so far, ranging from Spring MVC to a pure HTML5 based UI.
Please, have a look at http://forge.jboss.org/docs/important_plugins/ui-scaffolding.html and at the Forge source code itself to see how it's possible to create a new Scaffold based on your requirements and feel free to share to the community if you like.
If you have any questions, don't hesitate to look for us in this Forum or at #forge in irc.freenode.net