Theory of Emanation is simply the incarnation of the ideal Archetypes in the world of forms. On the other hand, evolutionary theory goes from the forms (matter) and becomes the "Archetype" (man).
It is a metaphysical theory that follows intelligent design. The flaws are a bad understanding or even a plain ignorance of evolutionary theory and the creation of an emanation Theory to fill the gaps.
To make this thread more useful and since the adherents of intelligent design have not made a concrete criticism, I'll start through one source given by nous in this thread.
SIX FUNDAMENTAL FLAWS IN
THE EVOLUTIONIST HYPOTHESIS
(1) Logical The greater cannot come from the lesser. (A biological example: The acorn gives rise to the oak-tree precisely because it already “is” an oak-tree. The acorn is not some nondescript “unicellular organ” or an ameba.)
(2) Physical (entropy; the second law of thermodynamics) Complexity tends towards degradation. Systems naturally move to a greater degree of randomness. Things run down, not up; they proceed from a state of order to a state of disorder. Order does not emerge from disorder (or organization from disorganization). Order is conferred on disorder by the input of “information” (“intelligence”), and cannot arise by chance. “Intelligence” is not the product of disorder! Nothing has ever been known to contravene this law, but the evolutionary hypothesis contradicts it.
(3) Biological (the stability of species) There is no conclusive evidence that one species ever changed into another. (If there were, evolutionists would trumpet it from the house-tops!) “Parents” have never been known to give rise to other than their own kind. (There is evidence only for intraspecific variation, not for the formation of new—and self-reproducing—species.) This is because of the fundamental “stability” of species. A species is a Platonic archetype. Evolutionists try to “blur” this as much as possible; some even deny the reality of species.
(4) Statistical (not enough time) Evolution requires that there should have been a spontaneous generation of life, but the simplest of living cells is so complex that the probabilities of its coming into existence by chance cannot be expressed in meaningful figures. No matter how much one extends—on a realistic basis—the time-scale envisaged, it is statistically impossible for the generation of life, and for evolution, to have taken place by chance in the time available. (The rather fantastical theory that life “may have come from outer space” merely sets the problem one stage further back; it does not solve it.)
(5) Teleological (the argument from design) “It is impossible that blind, deaf, and dumb evolution could have given rise to eye, ear, and voice.” “The miracle of consciousness did not arise from a heap of pebbles.”
(6) Philosophical (the relativist pitfall) The evolutionist hypothesis is fatally impaired by the well-known contradiction of relativism, often demonstrated by means of the statement “All men are liars.” (If they are, then this statement, also made by a man, is false.) Specifically, in the present case: man, who is said to be evolving (and is therefore relative), cannot all of a sudden step out of the evolutionary process, take up a stationary position, and dare to make absolute statements regarding the continuing process. It is this that is absurd.
For the theory of biological evolution to be sustainable, each one of the above objections must be refuted. This cannot be done. The evolutionists do not rise to this challenge. They look the other way, and bury their heads in the sand.
1) It depends on systems. The increasing complexity of the first life forms to humans, did not happen by a closed system process, but by a gradual fitting to other biological units and a reaction to the conditions of the environment. The cell is not isolated, and the cell doesn't become a man, but only through the interaction and fitting to other systems around it.
2) Evolution is about natural selection. Entropy is about the constant measure of energy within a system (heat) and it is not the same thing as disorder, specially because the Earth is not a closed system.
3) What about "transitional" species? The classic example being the Archeopteryx, or our hominid ancestors.
4) Again, confusing evolutionary theory and abiogenesis. This statistical argument is full of flaws:
-They calculate the probability of the formation of a "modern" protein, or even a complete bacterium with all "modern" proteins, by random events. This is not the abiogenesis theory at all.
-They assume that there is a fixed number of proteins, with fixed sequences for each protein, that are required for life.
-They calculate the probability of sequential trials, rather than simultaneous trials.
-They misunderstand what is meant by a probability calculation.
-They seriously underestimate the number of functional enzymes/ribozymes present in a group of random sequences.http://www.talkorigins.org/faqs/abioprob/abioprob.html#Intro
6)Unless the self awareness of man is an evolutionary achievement that grants his adaptability to the environment by a more efficient organization of brain cells, product of natural selection.