Request no.1 - different filenames for JAXB and JAXB 2.0
Original request - All jar files should have different names from JAXB 1.0 files. This will allow using old code alongside the new (during the transition phase).
Kohsuke comment - you can override JAXB 1.0's jaxb-impl.jar with JAXB 2.0's jaxb-impl.jar and jaxb1-impl.jar, and you can have old code along side the new one. (Or maybe alternatively should we name it jaxb2-impl.jar and jaxb-impl?) Do you still feel that we should be renaming jars?
In fact, this is exactly what i have done in order to be able to run both JAXB and JAXB 2.0 in the same project. As long as JAXBContext, Marshaller and Unmarshaller of JAXB 2.0 are backward-compatible, there should be no problem, although i don't know what is ClassLoader policy when it has two classes with the same name in two different jars.
The choice is up to you, but i think it would be more apropriate to use new name for JAXB 2.0 in order not to break existing build files.