IThat said, I never thought USNA set people up for success physically in the admissions process. The entry PT test is a joke and isn't representative of anything at USNA or in the fleet. A Basketball throw.... really? How about we just give prospective midshipmen an actual USNA PRT in the admissions process or actual USNA swim tests or even a 1st, 2nd, or 3rd class Navy swim test? These things already exist, why doesn't USNA use them? It's frustrating to see good mids get the boot for things that don't carry over into the fleet after commissioning. That's a leadership failure right there.
The reason USNA uses the CFA is that it was decided among USNA, USAFA, and USMA (not sure about USMMA; USCGA has its own test) that they would come up with one test so that candidates who apply to more than one SA (and there are many) don't have to take multiple tests that -- more or less -- measure the same thing, fitness. Thus the CFA was born.
It includes events that each SA wanted. As has been posted many times on these boards, USNA could care less about the basketball throw, but USMA wants it. So, everyone takes the whole CFA and each SA scores it as they see fit.
As for why the standards are what they are . . . . all SAs recognize that, with a concentrated PT program -- to which not all candidates have access -- fitness will improve. So, as long as someone is reasonably fit and has a general interest in sports/fitness, the SA can and will do the rest. Once you get to an SA, it's up to you to ensure you stay fit so you can pass the test your full four years.
Finally, as for swimming . . . USMA and USAFA could care less about swimming ability, at least to the extent USNA does. More importantly, it would be an administrative nightmare for USNA to require swimming tests as part of the application process. Let's face it, not everyone has easy access to any pool, let alone everyone having access to a lap pool of the exact same length in which to take the test. The fact is that, if you can swim when you arrive at USNA, you should be fine. You may not make As or Bs but you'll pass. If you've never swum before, you may struggle. USNA will teach you to swim but you may still struggle.
So, for those planning to attend USNA, if you are not comfortable swimming 200m at a "reasonable pace" without stopping, you may want to take a swimming lesson at your local YMCA/YWCA, etc. before showing up. And, before someone asks, I would define a "reasonable pace" as: if someone is watching you from the pool deck, they don't think you're going to die halfway through nor are you so slow that they can have lunch before you finish. Thus, a moderate pace where you aren't struggling is ok; you need not be the second coming of Michael Phelps.
I would agree that USNA could do a better job of making sure candidates are aware of the swim requirements. I typically discuss them with my candidates and, if they tell me they aren't comfortable in the water, suggest they might want to take a swim lesson.
Finally, fitness is important in the fleet; there are PT standards and people get kicked out for failing. Swimming is important for some disciplines (SEALs, Navy and USMC Air) but less for others. Still, when you're a water-based service, being able to swim is probably a good idea.