Each service has different medical standards (to an extent). For example, color blindness is a huge deal for sea-going services but not so much for Army and AF. Thus, the fact you received a waiver from USAFA has absolutely no bearing on whether you will or won't from USNA.
As for NASS, being selected (or not selected) is not a measure of competitiveness beyond a certain minimal level.
There are two sides to a medical waiver -- the medical condition itself and the competitiveness of the candidate. First, it has to be a waiverable condition. Something like diabetes is almost certain not to be waived no matter how great a candidate you are. As for waiverable conditions, the bottom line is that USNA wants to commission around 95% of the class into unrestricted line. Thus, they don't want too many folks on the front end with medically limiting conditions b/c they know some mids will develop them during their time at USNA. Thus, how terrific a candidate you are comes into play when USNA decides whether to give you that waiver and appoint you vs. giving it to someone else with the same or other limiting medical condition.
The sad but true fact is that, if you need a waiver for a condition that will limit your commissioning opportunities, it's harder to get in than if you don't. That said, lots of folks are successful and you may well be one of them.