putting asside the fact that large directories are
a bit dumb to begin with, there are other problems 
associated with them. Many software programs can't handle
the size, or redundantly crawl. This makes the local copy
difficult for the novice user.

(for example, I downloaded a forum of 13000+ files in one
directory, and K3B crashed trying to burn the thing
to CD.)

This is just a suggestion:

When a directory exceeds some small number (say 500),
start a randomly named subdirectory. Just how, is your
domain. Should it be an option, etc, etc.

This idea here is that what comes down ought to be usable.
Just imagine clicking (opening) this directory and the window freezes
(sometimes crashing) as it starts processing.