Paper on complexity by HerbertSimon.
Great discussion by PhilAgre : which http://polaris.gseis.ucla.edu/pagre/simon.html which raises conflict between "hierarchy" and SystemsTheory as two rival, over-general explanatory frameworks, and then tries to find a historical synthesis of them.
*In any event, the point is that the explanatory schemata of hierarchy and self-organization are not always at war. Their relationship is complex and variable. Both schemata are woven throughout Western culture, and both are capable of coming to the surface in a wide variety of ways when conditions are right. *
Also notes the way EdmundBurke's project of Conservatism is a continuous renegotiation between the two (BecomingConservative)
The problem with such general theories is that it is not clear if what they explain is really the nature of things or if it is more the nature of our cognition process. For example when Herb Simon sees hierarchies everywhere it might mean that our mind organizes things into hierarchies to manage them.
That's a point ChristopherAlexander also makes in ACityIsNotATree. But how does this worry differ from the same concern about any theory. For example, "when physicists see quarks everywhere it might mean that our mind organizes things by particles" (See also AtomismAndHolism)
All theories are products of the mind. And no theory captures the world exactly as it is. But I guess you are worrying that "hierarchies" and maybe "systems theory" are particularly bad. Is it just because they're particularly general?
When I think about this I think about mathematics. How much vaguer and lacking in concrete detail can you get than the number 3? I guess my point is that some models are good because they closely capture a lot of concrete detail. And some models are good because they are very abstract but allow certain kinds of reasoning which turns out to be very useful and applicable.
But I don't know of a good general way to tell which abstractions are going to work before-hand. Or that we can say much simply from how abstract they are.