I can confirm that /usr/local is there by default on a clean install of El Capitan
Re:El Capitan and Homebrew
by dpatriarche on Thursday October 01, 2015 @12:30PM
(#10312375)
On my Yosemite system /usr/local was created by default when the OS was installed.
If it exists, we can use it as before.
Considering how many times I've installed OS X, I can't recall if /usr/local is there by default (excluding 10.11 for the moment). Will have to do another few installs and check.