If we think of the core elements of protecting, connecting, and restoring landscapes, it's unquestionable that those sorts of coarse filters and fine filters of the ecosystem and species-based approaches have to go hand in glove. My understanding of the conservation biology literature is that in order to maintain the habitat that is going to maintain the broad swath of species, some of which we may not have even identified yet, we're going to have to take those ecosystem-based approaches.
At the same time, there are important reasons for picking focal species for planning purposes, both species that have large area-based needs that help us understand how much we need to set aside, as well as species that have special needs that are threatened or endangered.
The key piece here is a question of what might be called conservation design. What are the processes and mechanisms we need to put in place for land-use planning, spatially based cumulative effects assessment, that allow us to ask those questions and apply both lenses to the question?