How do Proteins migrate in MES vs. MOPS
Well, to rationalize everyone's comments, I think @leonardo is right.  

This is a denaturing SDA PAGE gel.  The migration of the SDS Micelles which are negatively charged, depends upon the shielding of the solution around it.  The difference in mobility is because the SDS micelles will experience a slightly different field at pH ~6.2 (MES) vs 7.2 (MOPS).  

The thought that these have the same charge would be right at exactly the pH corresponding to the pKa.  For these two ions the proportions will not be the same when running 0.8 pH units from their respective pKas. the ion concentration goes as +/- log ([BH]/[B-]) and the charge environment of the buffer should not be the same.  I think that the higher pH for MOPS running will tend to create more negative charge in the solution from MOPS- but also OH- in solution, slowing the mobility of the micelles and favoring the resolution of the larger proteins with MOPS. 

This is all given even if the buffering ion concentration is the same.  

I'm sure the gory details are buried in the musty tomes of some physical biochemistry journals deep in the library, but this is how it sounds to me.