My complaint is it should store each email in its own file (like NNTP readers do). This makes it much more amenable to backups, search, and makes it a lot less susceptible to corruption.

Instead, Tbird stores one folder in one gigantic file. One threading error, and poof! It's gone. Happened to me several times. Yes, I filed bug reports. No, it was never fixed (at least the Tbird developers denied this was a problem).

Another minor thing I'd like to see is don't hide everything in multiple places.

There's still no way to backup my account settings.