A compatibility layer (either in the same package or in a new namespace) can soon become very ugly, for example when you introduce new data structures. When such an compatibility layer would be absolutely necessary, my vote is: don't do the API changes unless the refactoring is not much more than method renamings.
Another option is a long transition phase with developer releases on CPAN. When you are happy with the new API, increment the major version number and release.
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