How often do you cycle apps? Since I joined PA Online, I've gone from Thunderbird to Sylpheed to Mutt. Thunderbird was using mbox-type storage (Helloooo... We're not in the 80's!), Sylpheed used a maildir-ish (separate file for each mail), and Mutt, well, Mutt does what you want it to. Which for me is maildir.
Why do we change apps anyway? Talk about a waste of time (import mail, get comfy with client, then throw it all away and start all over again). My guess is that I'm at least susceptible to the "grass is greener" problem of new software.