If, in fact, the qualifications of applicants were race-neutral, then this would make perfect sense. However, the reality is that blacks on average are less prepared for university than whites. There are a variety of reasons researchers have put forward to explain this, and many of them aren't based on genetics at all. For example, some postulate that black culture de-emphasizes the importance of education, and even stigmatizes it. Whatever the reasons actually are, the reality is that blacks of college-admission age are less prepared than whites.
Both blacks and whites are less prepared than Asian students (or Jewish students, from a religious perspective). Once again, most researchers postulate non-genetic, usually cultural, explanations for this. But whatever the reasons, Asians of college-admission age are, on average, more prepared than either blacks or whites.
To implement an affirmative action program that dictates admission and graduation outcomes when preparedness isn't race-neutral, obviously the standards for admission (and graduation) also cannot possibly be race-neutral. There is no other way to get equal outcomes when the “inputs” are unequal. Therefore admission standards under affirmative action programs are most difficult for Asians, and least difficult for blacks. That's pretty simple and straightforward – but it leads to outrage amongst the students held to a tougher standard, and amusing denials from the affirmative action crowd (who don't like to admit that they're fighting racial discrimination with more racial discrimination).
The solution seems obvious to me, and it's the same solution propounded by both Martin Luther King and Clarence Thomas: end discrimination of all kinds. As Thomas famously said:
...there is a 'moral and constitutional equivalence' between laws designed to subjugate a race and those that distribute benefits on the basis of race in order to foster some current notion of equality. Government cannot make us equal; it can only recognize, respect, and protect us as equal before the law. That affirmative action programs may have been motivated, in part, by good intentions cannot provide refuge from the principle that under our Constitution, the government may not make distinctions on the basis of race.