Dear WP,
I am sorry to read about your eyesight deficiency and I would LIKE my post to be helpful, but I am not sure you understand the system or the standards.
First, and maybe the least important detail, is the DoDMERB doesn't DECIDE the standards. If you sound out the "D o D M E R B" letters, it is in the end a REVIEW BOARD. They review. In this case they take your medical records on one side and the DoD standards on the other and they just give you an up or down vote if you meet the standards as written. There are written standards and unfortunately it sounds like your eye or eyes don't meet the standard. From your short post I'm not sure you understand that. It would be like you saying your gym teacher DECIDED you didn't meet the standards for the CFA. He just submits the scores.
If you are applying to more than one program, they will undoubtedly reach the same conclusion for West Point as they did for whatever program (ROTC?) you took the DoDMERB exam for initially. The standards are pretty much the same. You will only take one medical exam and those same results will be resubmitted to different programs (USNA, USAFA, ROTC).
The part that is most difficult to understand is that there is a waiver program, and the WAIVERS are different for each program. You may have an eye problem that is waiverable at one Academy and not at another. What really makes you scratch your head is when the Naval Academy says OK, and NROTC says no, or vice versa.
What can get you a waiver? Being a valuable candidate that will contribute to the Program. Probably too late for you to become an olympic swimmer or gymnast, but that helps. The Academies automatically consider you for a waiver. If you are too far out of physical limits (say, completely blind for instance) then you will probably not get a waiver. Also, if you are far out of standards for Academics (or fitness, or you have conduct problems), the Academy will stop the waiver process and let the "does not meet standards" ruling be final. If you are a strong candidate, shows interest, good inteviews, that should help.
That is not to say that this "does not meet standards-no waiver" is the last word. If they tell you you are blind but you know you can see, then you can, at your own expense, re-test and submit those result to rebutt the ruling.
There is no system or mechanism for influencing, appealing, or requesting a waiver. If they really want you, you may get one. Hope this helps.
Good luck.