I think the key is balance. You can be spending so much time looking at the system that you begin to lose species. When you lose a couple of key species, you can quickly lose a system.
So through a balanced approach I think you can retain both. You can spend some time on the most vulnerable species—not every individual species, but a couple of the most vulnerable that are perhaps representative of a certain type of habitat within a system—as well as look at the overall ecosystem.