I'm trying to get around this by switching my documentation to robodoc. The main advantage is to be somewhat more compatible with ctags; it also is compatible with many languages, and not only perl; and the default formatters (robodoc to html, etc) give better looking results than corresponding POD translations.
What I still miss is a practical robodoc-to-POD (and reverse) translator, though :)
update: I've finally made it ! It's fa for perfect but it works fine with all my code. See ROBODoc to Pod translator