I'd also suggest trying a recent version of gnus. If you're running Debian "apt-get install emacs21 gnus", and then "info gnus".
The standard nnml storage format is similar to what you're used to, but also includes a news style .overview file in each directory to speed things up. Gnus has backends for many other formats too, including mbox, imap, maildir, and slashdot, among others. You might also want to look in to the gnus agent (plugged vs unplugged), pgp handling, mime handling, stackable summary limits (limit to author, limit to...), process marks, attachments (C-c C-a when editing a message), etc.
Gnus does handle email in a potentially unusual way by default, but it's not too difficult to change that. For example, you can change it to mark articles as dormant, rather than read by default, when you read them so that they won't be subject to expiry. This presumes that you're using total-expire for the relevant group, which means that read email expires after N days. Given that alteration, then you'll just explicitly hit 'd' to mark an article as read, which will schedule it for expiry. Gnus' normal delay for deleting emails can be handy sometimes, but you can always force an immediate delete if you need to.
The only thing I can think of that you might be missing is command line email manipulations, but you can process mark any number of articles in a group with '#' and then most of the default operations will apply to all of the marked articles. You can also set the process mark according to various criteria, and you can always apply an arbitrary function to the process marked articles via M-&.
All that said, I'd also note that gnus is probably not for everyone. Anyone who prefers thunderbird/evolution style GUI clients is probably not going to be happy with gnus, and the learning curve for gnus is not nearly as shallow, but in exchange, gnus' flexibility is very high.
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