I have seen both systems at work although the system with the algae scrubber had few fish and nitrite levels kept at a minimum due to its lower feeding levels it also allowed the corals to feed more with out the the nutrients being skimmed out by a protein skimmer at the same time it also stabilizes your ph at night when your aquarium lights are off and your scrubber lights are on. A system with a protein skimmer can handle a heavier biological load and can easily remove waste and thus for lowering the nitrites and nitrates more effeciently. Corals are very sensitive to nitrites and a protein skimmer is almost a must for those involved in husbandry although some experimenting with scrubbers have succeeded quite well . I personally run both and I just turn off my protein skimmer when feeding my corals.