The truly good student is the one who signs up for the class with the goal of mastering the material being taught as well as possible. The 'good' student in this example cares more about gaming the signaling mechanism than actually learning the material - this is why he'll spend his time arguing with the TA over a handful of points on his problem set than spending that time going over the material again. The 'cynical bad' student is already convinced that he's not going to get anything out of the class, in which case he either 1). is taking the class because he has to or 2). is a fool who should be taking a class better serving his needs and not wasting his time.

Also, I don't know much about philosophy (and I suspect this is far less applicable for philosophy), but in science and engineering often mastery and innovation in a field requires an extremely narrow focus that, in turn, requires a significant investment in time and resources. This includes transmission of specialist knowledge to graduate students and postdocs, grant writing, paper publishing, acquisition of equipment or access to equipment. So I don't really think it's entirely fair to chalk up lack of interdisciplinary interest and/or innovative methodology predominantly to a system that weeds out people not willing to think the way it wants them to. (Not saying that tenure doesn't have its own problems...)