I think that it'll be difficult for you to get an idea of how the two compare since people on this forum have experiences with either one or the other. I go to a school with a sytem-based approach and personally I am very happy with this curriculum. It makes much more sense to me to learn everything about one organ system at a time: usually in the first week we learn normal physio and anatomy and then go on to study microbiology, path, and pharm. That way it's all organized in your head together. A big advantage of this is that second year in our school is actually pretty chill because we don't have to go through the hell of mind-numbing memorization of endless path, micro and pharm. Sure we still have to learn it but we get it in manageable doses with each system.
As for the boards, I think more depends on your own study habits than on the curriculum, but having said that, our school has switched from disciplines to systems five years ago and the average board score for our school has gone up 5 points EACH year ever since.