have an internet connection to stream and want to copy it to your iPad to watch later?
With an MKV, you've got to install a 3rd party app to play it back, and then take up 6-7GB of your device memory to watch it. Whereas with MP4/M4V it copies right into the Videos app, plays natively, and takes up less than 25% of the space.
If keeping everything in MKV works for you, great. But I wouldn't go around recommending it to everyone without knowing their plans on how they'll be watching it.