A lot of our customers that have switched to El Capitan are reporting problems, apparently because of rootless mode. Most are running Unix based stuff, which is often put in or uses some of the lower level directories. One of our customers disabled rootless and re-enabled it, and in doing so he claims it destroyed some symbolic links for X windows that had previously been there. It's beginning to look to me like rootless was not a good idea. I would guess about 15-20% of our customers using El Capitan are complaining.