Are you running any hacks on your Vita?
System Use is, basically, the "miscellaneous" files that the Vita's OS can't categorize as a game/app/whatever. For example, for me I have 2,152MB listed as "System Use" and a majority of those are ROMs for emulators on Henkaku.
If you are running hacks, simply clear out some of those files that you may have on there. Maybe it's PSP/PS1 games on TN-V or ARK, or like my example ROM files from emulators you might be running.
If you're not running hacks, then the only "solution" is to backup your games and saves with CMA and then reformat the memory card.