I believe the J2EE/JavaEE specifications designate packaging to an 'assembler' role for good reason. The code for web module and resource adapters (a real connector, not simply a configured JDBC pool) are managed well as plain jars. Dependencies are satisfied by external jars, and you have fine grained control over reuse. IMHO, making wars, rars, and ears first-class maven citizens seems a bit strange. The way you package them changes on the environment, Appserver, et cetera. The compiled code doesn't change.
I have used the rar, ear and war plugins to build both skinny and full-fledged components. I can appreciate why you would want to package the full fledged components (at least war and rar) because they are reusable components much like the jar. They are intended to be boxed up and reused. However, these components imply configuration and repackaging (Class-Path entries in the manifests of modules, moving jars to ear-level, changing init-params, configuring security, adding appserver specific descriptors, etc). This seems to indicate that they are not artifacts in the traditional maven sense. They are not static like jars, so storing them as such doesn't make much sense. It may not make sense to store them with the jar dependencies bundled; this is like storing uberjars all over the place. Perhaps the realization of an war/ear with dependencies is better deferred?
Wars and rars are ideally treated as components. So it may make sense to store them with their external dependencies. However, I believe dependency meta data could be used. This would perhaps be something like a dependency scope 'aggregate'? It would imply that transitivity blocks at the artifact that aggregates them. Unfortunately, if dependency meta data isn't available to dependent artifacts you can no longer identify or resolve conflicts, et cetera. If you could use this meta data, then you could perhaps control the ultimate fate of the dependencies through something like dependencyManagement. It may be enough information for an intelligent assembly plugin to realize the aggregate dependencies and patch up bundled modules with Class-Path manifest entries, et cetera.