[toast0]

If you've got 1M files, your alternatives include:

a) 1M files in a single directory

b) 1k directories with 1k files in each

c) 1k aggregate files with 1k files in each

d) 1 aggregate file with 1M files in it

I think there's some filesystems that will work with option a, but any filesystem should work ok with the other options. Options c and d will make rsync much faster as you eliminate millions of syscalls.