What's up with the "System Use" thing in PS Vita's Content Manager?
"System Use" could refer to firmware updates and system software, updates / patches to system applications, or temporary or other system related data (e.g. cached information, system files etc). You can't clear / flush this data directly.
However, you can try using the Safe Mode to "Rebuild the Database" to see if it can clear up some of the space.
To activate Safe Mode, press "R" button + PS button + Power button while the console is turned off. Once in Safe Mode, use Option 2 "Rebuild Database".