You've not been the first (Or the last I would guess) who has suggested amplifying POD. Though I have strong objections to altering POD (many of which have been already cogently made. Thank you podmaster.) there are some interesting ideas to be discussed. POD Is Not Literate Programming at perl.com is an excellent discussion of some of these ideas.
The best solution to the problem, as we seem to be converging upon it, is to have a "POD preprocessor" that parses a superset of POD in a program and alters it for inclusion in a distributed module or the like. This would be a useful tool for the programmer, and make documenting the code easier, but wouldn't break POD's unique uses as a markup or even alter it at all.