I liked that Mail.app stored every message as a single separate file, instead of the mbox that Thunderbird and others did. But at some version they started saving a hash with a multiple folder structure and that broke the setup. I had a few issues with MIME encoding as well, which were probably my fault. It was too much work and I eventually gave up, but if I find the will to do it again, I'd choose a simple POP downloader + some filter (if not in address book or previous recipients, move message to “Unknown”).
qlmanage worked great for HTML messages and attachments, though.