Application, folks, application!
For shooting at prarrie dogs, the 5.56 is generally the better choice, because it has more appropriate bullets available for it. NOTE: the last thing you want for hunting p-dogs is a 75-77gr bullet; think 50-60gr VMax or BlitzKing.
The 6.8 SPC was developed to be a COMBAT load, and it is excellent at that (and coincidentally, excellent for hunting medium-sized game like deer and hogs), but its strengths aren't as apparent when hunting p-dogs. Varmint-sized animals are really what most 5.56-class ammo is best at.
-Troy