My guess (again assuming the ratings do/well be patched to do anything) is that AGI would matter with changing directions on cuts. Like if the WR is running straight upfield, but then makes a good cut ot the inside, AGI would impact how well the CB changes direction.
Meanwhile the MCV rating would allow him to be more successful batting down the ball, etc. So a guy with good AGI but bad MCV wouldn't make many plays on the ball (deflections, reaching, etc), but he'll be all over the WR and might take him away that way (i.e. the QB reads it as a bad risk and looks elsewhere).
We've seen guys in the real game that have been all over the WR but the ball still gets in there because he's late with the swat or isn't in the best position to make the play - those things could be impacted by MCV.