We are rather dissatisfied with our commentary earlier regarding preserving aboriginal culture and the importance of New World archaeology as a whole. Well, actually just the latter.
The reason the isolation we mentioned is so important is that, essentially, it doubles our sample size for comparing the rise of complex civilizations (among many other problems). Basically, without it we'd have nothing to compare. This is the problem origins-of-life people are having, as the total sample size for Places Where Life Arose currently stands at 1. Thus, any hypotheses one wishes to test regarding the orign/development of complex culture can at least be tested in two different places. This can't really be so in the Old World generally, with a few exceptions in a few places over time. There was simply too much interaction.
Example: Agriculture. The bulk of domesticated species, and perhaps even the idea of intensive agriculture as a dominant subsistence strategy, probably arose in the Near East and spread out from there to the remainder of the Old World (southeast asia excepted to a point). One can even trace the diffusion of agriculture out from the Near East as a rather nice wave. But since the New World was isolated at this point, one can also look at how agriculture developed there without any possible contaminating effects from the Old World centers. Consequently, any general theories of agricultural origins must be tested against two areas. This is not only scientifically desirable, but it also keeps archaeologists from becoming too dependent on one set of data for their theory-building exercises.
This 'comparitive method' (almost a discipline unto itself) also functions nicely for other cultural features. Ceramics were both invented in the New and Old Worlds independently of one another. They tend to be very similar in many ways -- everybody figured out that adding certain materials such as sand or crushed shell as temper will affect the functional parameters of the finished vessels -- but there are notable differences. The most obvious is that the New World never developed wheel-thrown pottery.
The impression we get from history, traditionally, is that the New World populations were essentially Stone Age peoples compared to Europeans of the time. In some sense, this is true since much of the New World populations still relied on chipped stone tools, never having developed metalworking. But this (among other problems) assumes a linear trajectory of cultural evolution. That is, it was assumed (still is in some quarters) that every culture must go through the same "stages", all heading inexorably towards what modern Anglo-European civilization has become. But who knows where New World civilization had gone if contact had never occurred.
It's also the crux of many comparisions between Old and New World archaeology. Why didn't they develop writing systems? Or metalworking? Why were they comparitively "late" in obtaining certain technologies compared to their Old World counterparts? We all got largely the same start at the end of the Pleistocene with late Paleolithic hunter-gatherers, so why were Old World populations sailing large ships across the globe while aboriginal Americans were still using stone tools? Many generations of scholars have worked on this, and progress is painfully slow but it remains one of the preeminent issues in the sudy of mankind.