1.) Demography: Who is the ideal MBA candidate? From what I've gathered, the historical answer would be: "Someone from outside a business education about to move into a business role." So, of course, your average MBA is going to be someone who studied Biology or Mechanical Engineering as an undergrad, right? Well, they're in there, but they're surrounded by people who studied Business and Economics as undergraduates, often from elite schools! What could a Wharton undergrad possible gain from a Wharton MBA? Social proof? A two-year vacation? It's unsettling, and it leads to the second problem.
2.) Intent: What sort of work is the MBA cut out for? Well, they're masters of administrating businesses, so...management? Nope. Consulting and banking. Like lemmings, they go right off the cliff into these fields. All of them. Even the ones who came in there looking to simply move up the ladder in their chosen field, like biotech or energy, will feel pressured into becoming some sort of banker or consultant. So, the MBA ends up becoming a launching pad for people outside of consulting and banking to get in, and for people on the inside to move up.
I don't know how business schools would go about rectifying these flaws. Even if they were to shut out business types, that second flaw is so deeply ingrained in the b-school ethos that anyone seeking to be a better manager in their original field would likely be derided by his or her peers as an underachiever.
Interestingly enough, I hear the Executive MBA is a far better experience, simply because the students are too far along in their careers to make a pivot into something else. They're just there to get better. And maybe for the two-year vacation thing as well.