You'll notice that we also use binding.soap instead of binding.ws. The main reason for this is that implementation.java and binding.ws are SCA standards and the configuration and expected behavior are constrained by SCA specs. It would be great to get to a point where our Bean and SOAP components fully support these standards, but that is not the case right now. So we are using implementation.bean (with SwitchYard specific annotations) and binding.soap to avoid confusion until we can support the standard behavior of these components in SCA.
As you noticed, the Java annotations are basically the same, so it should be easy for user's to switch over. We may keep the bean component stuff around if we decide we want SwitchYard specific functionality associated with service beans (ala Hibernate -> JPA).