I know the general versioning problem is address through the tool-shed mechanism, but for the remaining core wrappers, can maintainersplease update wrapper version numbers when making changes?

Not bumping wrapper versions is an oversight, not deliberate.

For this wrapper set, how would you advise us to support both?

Fortunately, I refactored the Cuffdiff wrapper recently and correctly bumped the tool version:

https://bitbucket.org/galaxy/galaxy-central/commits/6a32d26aefc758cf576e0b753c2626ac56005c18

You can either pull this changeset manually or wait until the next distribution in early October to get the changeset.

Best,