/System/Library/LaunchAgents is locked in El Capitan
El Capitan adds a new security feature named System Integrity Protection (SIP). Among other things, SIP prevents parties other than Apple from adding, deleting or modifying directories and files stored in certain directories:

/bin
/sbin
/usr
/System


Apple has indicated that the following directories are available for developers to access:

/usr/local
/Applications
/Library
~/Library


All directories in /usr except for /usr/local are protected by SIP.