MP4 is the world's default video: the file that plays before anyone has to think about it. It was born in 2001, the MPEG standards group, built on Apple's QuickTime design, and its real weak spot is very little day to day: as a container its quality depends on the codec inside.
FLV is a relic of the Flash era: the format YouTube grew up on, stranded when Flash died. The Flash Video container, typically holding old H.263, VP6 or early H.264 streams. That makes it the right destination when what you need is nothing new: today it's mostly old downloads waiting to be rescued.