My short answer would be that it's not a choice between quality and quantity; we need both.
We need to make sure that we're selecting areas that are of high ecological value. In many cases, those are the large intact wilderness areas that still remain—places such as the boreal forest of Canada, for instance, which supports woodland caribou. They need large areas because they have very large ranges. If we want to protect that species, we need to be selecting the best habitat and ensuring that there's enough of it.