It was just pure entertainment, not history
There was always an element of unrealism to BAA BAA BLACK SHEEP, with the hard-drinking, frat-boy partying, mischevious ways of the Marine pilots depicted in the television series. Anyone who has ever encountered the U.S. Marines in real life know that these people pride themselves on individual and team discipline. That's not to say that Marines don't enjoy themselves off-duty and off-post, but they're not reckless as the show made them out to be. I've personally encountered a few U.S. Marines in real-life and all of those distinct individuals impressed me by their courtesy and proper behavior. Of course, I've luckily never encountered a drunk Marine.
BAA BAA BLACK SHEEP could have been more and better but it seemed like its creators had little military experience themselves. Also, the American involvement in Vietnam had officially ended in the summer of 1973 and bitter memories of the public divisions, emotions, protests, scandals, and more led the U.S. military to fade for a time behind the public consciousness. Patriotic and realistic gritty fighting movies like, "Saving Private Ryan" were in the distant future. Compared to 2012, the action and violence depicted on the tv show is astonishingly bloodless.
What few people knew at the time was that the actual Major Greg 'Pappy' Boyington was shot down and captured by the Japanese in early 1944. If the show was going to be historically relevant, it would have been difficult to carry the show forward through 1945. Hence, the timeline of the tv show seemed to be stuck in early 1944, when the U.S. was clearly starting to win but the Japanese still retained significant fighting strength in the outer Southwest Pacific, which all but collapsed by the end of 1944. So that is why the tv series Pappy and his flying Marine pilots kept encountering so many Japanese antagonists, some of which were skilled pilots. In retrospect, it might have been possible to ignore the actual history and carry the show into 1945 but after three seasons, low ratings canceled the show, making the issue moot.
I think the show could have been a little more 'edgy' and thus successful. But the time period just wasn't right for it. The show had its good characters and some weak ones. A few of the Marine pilots depicted seemed questionable. The ill-disciplined, canterkerous, and oft-insubordinate master gunny sergeant Micklin was a complete Hollywood fabrication which likes to think such individuals can actually exist in the military to poke an thumb in the eye of the military brass. Micklin, I think, represented liberal Hollywood's disdain for the military and its culture of discipline by introducing an indisciplined individual. In real life, wartime or not, a guy like Micklin maybe, just maybe might have gotten away with some of that reproachable insubordination, but never near as long as Micklin did in the show. The U.S. Marines would have never tolerated a person like Micklin, at least not for long. Micklin was not only brazenly insubordinate, he was borderline psycho. Guys like him end up fast usually dead in combat, bounced out the military, or confined for years at Fort Leavenworth prison. Also, in the real-world U.S. Marines, senior non-commissioned officers serve as examples of individual and team discipline and dignified pride, not do the opposite. But well, this is after all, Hollywood, and through time and space, Hollywood has been alternately pro and anti-military, with an odd mixture of both today.