According to (USNA Professor) Fleming, the admissions system is two-tiered because minority candidates have lower test scores and grades than their counterparts. In short, Fleming says that the Academy is rejecting better qualified white applicants to admit minority candidates with less impressive credentials.
The most pernicious effect of affirmative action plays out in Annapolis:
The environment is particularly toxic for talented black midshipmen...because they are perceived by some classmates as less-qualified.
And why wouldn't they be perceived thusly? Affirmative action, as practiced today, is bad enough because it legally discriminates against people on the basis of their skin color, but when you add in the cost to those it's designed to help, it's even more indefensible.