AAC is MP3's better-trained successor: cleaner sound from the same number of bits. It was born in 1997, an MPEG all-star team: Fraunhofer, Dolby, Sony, AT&T and Nokia, and its real weak spot is older or stubborn hardware that only ever learned MP3.
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.