For me the packaging would take a shape that supports the goals of deployment and version/change impact. For example, a single EAR is easier to deploy, download and distribute.
The only time I would unbundle the EAR is because one layer was changing at a different rate to the other and therefore they needed to be deployed separately. For example, the back-end services are stable but the UI keeps changing.
Of course, if you have a presentation tier that doesn't support EAR deployments, then the choice is pretty clear.