I'm 3/4 of the way through KCUMB's pre-clinical years, and here are just a couple of snippets of my thoughts on systems vs. discipline based.
1. Biochemistry might be the one standout that I think needs its own discipline based course. For me, at least, it is the one thing that I tend to forget the quickest, and thus is harder for me to make the connections from one system to another when biochem lectures might be many weeks apart. On the other hand, I actually understand how the pathway/enzymes/metabolites/regulation etc. interact with the body physiologically, pharmacologically, pathologically etc. during any one lecture. I just tend to forget the details, or sometimes don't realize how one pathway is connected to another. Not a big deal, really... see point 2.
2. IMO, however your school teaches I think you will benefit from doing board review in the opposite way. i.e., since we are systems based, I have a terrific big picture view, understanding of integration, and can work through most case based problems with ease; but I am finding it of benefit to do some board review in a subject specific way... physiology, pharmacology, pathology, biochem, etc. I pick up a few more details that at the time didn't jump out at me... but now that I have the big picture, I realize how some of them fit into the puzzle. On the other hand, most schools are still on a discipline based traditional approach, and most students find systems based board review books extremely helpful. So ultimately, I think both approaches are very useful to the student and will probably help solidify your understanding... whichever your school does, spend a decent amount of time self-studying in the other way for boards. Personally, I'd rather have systems based curriculum first because it gives me a very solid conceptual foundation (with plenty of detail), and is making self-studying in focused areas very productive.
3. Systems based rocks as far as keeping variety in your life. And I might be out of my mind, but it seems easy to keep up with and study for. Either that, or KCUMB is just a terribly easy school. I sometimes wonder if I'm learning half what other students at more traditional schools are, but then I do a few review questions from robbins or elselvier and figure I'm not doing so bad after all. I think it just seems easier because more stuff just "sticks" from exposure rather than from cramming charts and lists into your head.