MKV files are great — the format offers excellent compression and high quality video bit for bit. I do find that when I try to play MKV files on my Blu-Ray or Samsung TV (via USB device) it will not fast forward or rewind. The fix is to change the container to an mpeg 4 video container.
Here’s the simple command: (-threads 0 = use all CPU cores)
ffmpeg -threads 0 -i input.mkv -vcodec copy -acodec copy -absf aac_adtstoasc output.m4v