I don't think any reasonable person questions or has an issue with the zone. I think some (myself included) question the zone, nothing but the zone, so help you god style that JB employs. At times, there are advantages for sure, but if it was such an incredible defense, I think others coaches would also use it 100% too & copy the 'genius' that is JB.
As we all know, what matters the most is winning, and if it was such a precious gem D, more schools/coaches would play it 100%. I don't know of any other school that plays zone 100% of the time. I think like many sports, you have to play 'situational ball.' We don't, no matter what the situation (other than desperation pressing mode) is, we stay in zone. Situational ball is critical, whether it's baseball, hoops, football, etc. If it weren't, why do football teams shift from zone, nickle, man, etc. Why in baseball, depending on inning, number of runs down/up infielder's/outfielder's play up, vs. deep, etc. Same principle in hoops...