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.

FYI, the maildir format (usable with mutt and numerous other email clients) also saves each email message as an individual file, and avoids mbox's notorious quoting issue.

<https://en.wikipedia.org/wiki/Maildir>