If you're seeing stuttering in any MKV videos you've ripped, try out wipe0wt's suggestion and turn off loop filters in VLC altogether. It results in a dramatic improvement in playback quality. The gist is:
- Open up VLC and choose Tools -> Preferences from the menu
- In the bottom left corner of the preferences window you'll see a "Show settings" area. Make sure you change it from "Simple" to "All". This will change the left side of the preferences window so it's a tree view instead of a collection of icons.
- Navigate to the following preferences group from the tree on the left: Input / Codecs -> Video codecs -> FFmpeg. The right side of the preferences window will now change to "FFmpeg audio/video decoder".
- Check the "Allow speed tricks" checkbox
- Set the "Skip the loop filter for H.264 decoding" to "All"
- Click on the Save button on the bottom right of the preferences window.