1. Build a better computer
2. Use different encoding settings
And that's really all you can do. I currently can encode HD 1080p MKV Blu-ray rips (full size 15 - 35GB each) to 720p xbox 360 compatible in just a couple hours. But greatly depends on what processing power you have, your encoding settings.
Just need a more cpu. I am testing Handbrake tonight on a 4 core i5 Sandybridge. I now have a AMD 6core 1100Black cpu and it took Handbrake 1 hour 57 min to encode a 12GB 1080p mkv file(avatar) it took 40 min for MKV to rip the BD disk. That 6 core is a beast. My gut tells me the SB 4 core won't be to far behind.
Should have the numbers on the SB in the next day or so.
If MKV and MP4 are both containers then u don't have to transcode at all (where it takes the most time), you would just have to UNPACK the MVK to its components, then REPACK to MP4. Again *if* (I don't know) both of those are containers only.