Our curriculum is systems based and I like it. It seems easier to "connect the dots" based on the way we are being taught, but I have nothing to compare to besides FUN 1 and 2 which are similar to non-system based (i think).
Anyways, a typical module is set up so that we have anatomy and phys the first two weeks followed by pathophys for the last 3 weeks. Most of the micro, biochem, pharm, ect is included in the pathophys section. For ex, in the cardio module we would have lectures on pathophys of CHF, then diagnosis, then treatment of CHF, and then move on to the next topic.