Yes, you can get waived for one academy and not another. They all have different medical standards, but none of them are exactly more difficult, it just depends on the issue. However, whether they request a waiver or not depends on how competitive you are. It is possible (usually rare) for one to be competitive for one academy, but not another.
Currently, I am only waived for USMA (my first choice). My USNA and USAFA waiver processes have not even started. Mainly because I have not finished my USAFA application (it's my last choice), and I was told that USNA will not begin until my file is reviewed, which will not be until I have a nomination. Nominations for my state will either come out right before Christmas or anywhere from early-mid January. So, I may or may not get waived for those academies.
