|FAT12, FAT16 and FAT32 have some file size limitations and possibly file name character limitations which may or may not come into play. |
Other than that your files can be kept on any of those file systems.
Look at the chart in the link below.
All that said, using flash drives for storage purposes is a bad idea, IMO. They are the least reliable of any modern media. Possibly a close second are memory cards.
All storage media can and will fail, break, get lost or stolen, etc. you should maintain at least two copies of any data you wish to keep.