One of the main problems with academia these days, as I see it, is what I've taken to calling the corporate model. It's the notion that a university is essentially a sort of company and should be run accordingly. The major problem with this, of course, is that the university isn't a capitalist enterprise that exists to maximize monetary profit.
Another problem is that the people pushing this model often have an antediluvian understanding of how good companies work. I don't know much about business, but anyone who's ever dipped into the business pages knows that good managers these days don't simply expect to give orders and have them unthinkingly obeyed. Promoters of the "corporate model" on campus too often seem to have an industrial age factory in mind, rather than the more flexible, transparent, and even democratic corporate culture in the most successful companies today. That is, some promoters of the corporate model don't only fail to understand universities: they fail to understand companies. For more on corporate flexibility, check out this recent article, "Fostering a Culture of Dissent", from the NY Times business section.
Okay, enough for today: too much caffeine meant too much blogging.