Nobody's slipping through anything. There are now 3 classes of APAP going, the first to graduate June 1 (me--yay!) All of us so far have taken the MCAT. So far board scores have been good to off the charts. All 7 of us on c/o 2014 have gotten our first choice residencies and proved our mettle.
The rationale for replacing MCAT with PANCE/PANRE and solid PA grades is that there are so many highly qualified applicants who would make great docs but who lack an MCAT score. It's a hurdle that doesn't predict how well we do as a group. I'm sure a couple of my APAP classmates had good to great MCATs because they are that smart (and younger with less time out of school) but it's just not relevant. MCAT has some correlation with performance in preclinical sciences. After that the association REALLY drops off.
For us PAs, though, we have demonstrated an association between success on PA boards (PANCE/PANRE) and strong performance on step 2, NBME shelf exams, clinical rotations and medical decision making that I expect to carry through to step 3.
Y'all are welcome to try the PANCE instead of MCAT and see how you fare. (A light jest since you can't take it without certification of eligibility from your completed PA program.) My thinly veiled point here is that the PA applicants have already demonstrated a level of clinical competency that the other candidates haven't. We are different applicants and that's why LECOM views us differently.