I use Subler to remux mkv's to mp4. This is an extremely fast process and takes only 1 minute or so. If the audio source of your mkv is not AAC you will need to separately rip the audio and then re-add it to your mp4. To do this I use mpegstreamclip (the beta version has mkv support). Finally, if you want metadata to be added, videomonkey does this well. So in total:
1) Use subler to remux mkv to mp4 (if required extract audio from mkv file using mpegstreamclip and add the resulting m4a file to your subler project)
2) Run resulting mp4 through videomonkey to input metadata.
If the resulting file does not add to your iPad you'll need to use a hex editor to change a setting in the mp4.
The entire process is still faster than re-encoding and does not result in much, if any, quality degradation.