I would be helpful if you could define multiple releases per version. For Example: 3.0 (Version)

_ 3.0 RC1 (Release)

_ 3.0 RC2 (Release)

_ 3.0 Final (Release)

This would enable logging issues against the release (1.0 RC1 etc) rather than the version and still be able to generate release notes for the version which would include all issues logged againts all releases for the version. This would also be helpful for using JIRA for planning. You could schedule each release and track progress by release. You should be able see overall progress for the version as well.