MKV file sizes are outrageously large. MP4 is a great alternative (less than half the file size) that doesn't sacrifice resolution. With that said, not sure if it supports multiple audio tracks, subtitles, etc.
MKV is a container format, not a codec. It's great, and can contain an arbitrary number of audio, video, subtitle, etc tracks. This is why the file sizes can generally end up inflated, people will put all dubs and subtitles into one file. The video stream rarely has anything to do with this (other than the tendency for very high def rips to use mkv).
Secondly, mp4 is a container format as well, but is less generic. MPEG-4 is actually a series of standards. MPEG-4 Part 14 describes the mp4 container format, and MPEG-4 Part 10 describes the H.264 codec.
Only if the actual content (video bitrate etc.) differs. If you stick the same video in both MKV and MP4 containers, the resulting filesizes will be almost identical.
