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.
MKV is the format that hoards: video, a dozen audio tracks and every subtitle, all in one box. The Matroska container: it will hold practically any codec ever made. That makes it the right destination when what you need is high-quality rips and archives with multiple audio and subtitle tracks.