Hello,
I just updated an old MacBook Pro to El Capitan (that's the latest I can put there) and my old backup script stopped working.
I am doing backups with rsync to a NTFS-formatted disk. After updating OS X, I used the Control Panel to auto-upgrade FUSE for OS X at the latest version (3.5.4) and then I followed the instructions at https://github.com/osxfuse/osxfuse/wiki/NTFS-3G to install Homebrew and NTFS-3G. I didn't like the idea of changing Apple's original mounter, so I mounted my disk with:

sudo mkdir /Volumes/NTFS
sudo /usr/local/bin/ntfs-3g /dev/disk1s1 /Volumes/NTFS -olocal -oallow_other

Now, when I run rsync to backup my files, it will complain about not being able to set the permissions/owner/group of the files, and all newly copied files will not keep their original timestamp, but will appear as just created. Moreover, rsync will try to copy those files again at every run, possibly because the file timestamps don't match.
But, if I run rsync as root via sudo, all will be well.
Maybe that's how it is supposed to work, but it didn't work like that in my previous OS X 10.7 installation, so I thought I'd report it.
Thanks