I understand the frustration with receiving an LOA and being told that the waiver is very common to get. You have to understand that admissions just sees the disqualification code and verbiage, and also sees what get waived, but they are not familiar with all the intricacies that go along with certain disqualifications. He was considered for a waiver, the waiver authorities felt they had to deny it.
In this case, based on the information that was posted here, the corrected vision was 20/40 (disqualification for corrected distant visual acuity not correctable to 20/20) and anisometropia (anisometropia in excess of 3.50 diopters). It was never stated how much of a difference between the right and left eye for the anisometropia, but for the distant visual acuity not correctable to 20/20, the fact that the vision is only correctable to 20/40 is pretty high.
Just with the distant visual acuity only correcting to 20/40, you would never be able to be commissioned at an unrestricted line officer. The Naval Academy wants all midshipmen to be commissioned as unrestricted line officers. So from that point you are already in a bad position.
The admissions office does not have access to view an applicants medical record, so unless they were told, they would never have known what the severity of this was. I have to believe that even if they were told, 90% of the admissions officers wouldn't have a clue what they were looking at, or what it would mean. They just know they have seen waiver for this in the past, and to hazard a guess I would have to say it was for applicants whose distant visual acuity corrected to 20/25.
There is no list of disqualifications that can not be granted a waiver. There are a bunch of disqualifications where it depends on the severity of disease/vision issue/medical issue where some will receive a waiver and others will not. The disqualifications here are 2 of those types. As I've stated in this forum many times, the waiver authorities review each case closely, because everyone is an individual, and even though 2 people may have the same disqualification, the medical specifics for each individual may vary greatly.
I hope this helps you to understand the process that goes on behind the scenes, as well as to why this particular waiver was denied.
As always, if you have more questions, or if I haven't explained it clearly enough, please let me know and I'll attempt to have it make sense.