Im at a subject based school. What I do not like is that there tends to be a lot of overlap between subjects. I find this especially true in histology where they try to describe structure with tidbits of function. Yet we obviously talk a lot about function in physiology (and to some extent in biochemistry for cellular function). So the subject based method seems a little inefficient.
I'm not sure how system based schools test their students (is it 1 single test?), but we have a test for each subject. If systems based is just one test, I think that would be a benefit. I hate having 4 exams per week. I would rather have most of the week to study for 1 big all day test. I think this would also better prepare people for the boards.