I have to check this. Every time. I can't help it. My brain forces me to do it.
However, I have not quite grasped what it does. Why would I not want maximum quality, and why is it separate from the "target bitrate" and all the other quality-related controls? Why a "checkbox"?
The checkbox is there to set it to MRQ if you do not have a GPU certified card.
If you do not want to set all the controls every time you can make a preset.
MRQ is most effective when scaling from HD to SD. Todd Kopriva has a really good blog post about it here:
It's in the first post about scaling in CS5, CS5.5 and CS6.