First, as was noted in a 2002 HCN interview with conservation biologist Michael Soule, the "pristine ecosystem" that the 1962 Leopold report set as a target goal for the National Park Service was in fact something of a fantasy. The Park Service has never adjusted to the recognition that the early 19th century landscapes were wildly out of any equilibrium due to diseases decimating Native American populations. These conditions could never be sustained. Furthermore, the more stable patterns from about 1490 or so were developed by extensive Indian management, most obviously in the use of fire but also in other horticultural pursuits that now are abandoned. Thus any landscape in human memory was gardened in some fashion; without recognition of this history, the Park Service's management of its biota will remain unrealistic.
Second, there is a hint of the idea that ecosystems are a unit that will travel as climates change. This is untrue, and the evidence is in the record of ecosystems during the last glacial maximum. For instance, in southern Nevada, rat middens record the coexistence of species that today live in very separate environments. Individual species, not entire ecosystems, react to changes in the environment, so unless you know what every species is sensitive to, you cannot easily anticipate moving things around. Probably the best we can do is to open up corridors for biota to move freely, rather along the lines The Nature Conservancy appears to be considering.
Third, the issue of exotics is overblown. It should be easy to distinguish plants and animals exotic to the Americas from biota native to the New World. The former should continue to be discouraged, while the latter should be welcomed. While there is real concern that fragmentation of modern habitats and the pace of global climate change might impede natural responses, North American ecosystems have responded to substantial changes in the past through shifts in position and interaction; we should strive to accommodate such shifts to the greatest degree possible.
Interestingly, when I present this set of perspectives and issues to an introductory historical geology class and offer them choices on how they think lands should be managed, they distinctly prefer that wildernesses be allowed to change without human intervention, despite their recognition that the resulting ecosystems will not necessarily resemble any that existed in the past. The people charged with the actual task of managing these lands need to define such a broad vision, in essence revisiting the Leopold commission in the light of both new scholarship and new challenges. Such a vision will ease nuts-and-bolts decisions on the ground, much as the Leopold report led to rapid changes in the Park Service's management of resources.