I doubt that using org.wildfly for all new packages makes sense (or is
even being proposed.) Within a given module I'd rather see a coherent
set of packages than a semi-random split based on when a package came
in. So if some new functionality comes into a module with a coherent set
of org.wildfly packages, fine. But if it sprinkles random org.wildfly
stuff around instead of putting pieces in the logical spots in the
existing org.jboss.as tree, that's wrong.

I agree. In the transactions project we have a mix of com.arjuna, com.hp.mw, org.jboss and probably some other packages that don't spring to mind at the moment. It can be annoying at times, especially when they fall under the same src root. We had the option to fix this with version 5 of Narayana, but we decided not to do it. This was because we didn't want to make it harder to back port features and to search through the history. 

Personally, I'd only want to use org.wildfly for new projects where I'm starting from scratch. I just don't feel the rename buys you enough, to warrant the cost of harder back-porting and more complex history.