I really like the idea, and it would be fairly easy to implement. The only thing I'm not sure about is all of the extra file_exists() calls. Every place this was used it would need to do a file_exists to see if a modded version exists. Since we have a header/footer and the body template, you'd be looking at 3 file_exists for the templates and 1 for the script, for a total of 4 for every page load. I'd need to do some benchmarking and see what type of impact this would cause on a busy forum.
