* Big lecture classes, where a professor delivers canned lectures to enormous crowds of people as though we still lived before the invention of online video and the printing press. As far as I can tell, this is strictly inferior to having a really good teacher record lectures, then put them online. Preferably with an option to play them at 1.4--2x speed. This would also free up time and resources to focus on the parts of the educational experience where college can be better than online lecture videos plus a textbook.
* Often, a whole class of people has to proceed through a set list of topics in lock-step. Some people will find this too slow, and others too fast, for any given topic. What if you want some time to really think through a particular topic? There's no time; you've got to go on to the next thing. And then at the end of the semester, there's a flurry of activity as people finish up final projects and study for exams, and then BAM! It's over!
* The workload tends to be heavily skewed to the end of the semester, so people seldom have enough time to devote to finishing projects properly. This has caused no end of frustration.
* People are crazy-focused on grades, often at the expense of their education. Grades are a clumsy proxy for learning. It's like trying to measure someone's happiness by how much they smile: there's a correlation, sure, but telling someone to smile more is not the best way to make them happier.
I could list more, but that should be enough for starters. Would you dispute the claim that such a system is at least a little broken? Or, if you prefer, blatantly sub-optimal?