The principle upon which I understand the Natural System of Botany to be founded is, that the affinities of plants may be determined by a consideration of all the points of resemblance between their various parts, properties, and qualities; that thence an arrangement may be deduced in which those species will be placed next each other which have the greatest degree of relationship; and that consequently the quality or structure of an imperfectly known plant may be determined by those of another which is well known. Hence arises its superiority over arbitrary or artificial systems, such as that of Linnaeus, in which there is no combination of ideas, but which are mere collections of isolated facts, not having any distinct relation to each other.
This is the only intelligible meaning that can be attached to the term, Natural System, of which Nature herself, who creates species only, knows nothing. Our genera, orders, classes, and the like, are mere contrivances to facilitate the arrangement of our ideas with regard to species. A genus, order, or class, is therefore called natural, not because it exists in Nature, but because it comprehends species naturally resembling each other more than they resemble any thing else.
The advantages of such a system, in applying Botany to useful purposes, are immense, especially to medical men, with whole profession the science has always been identified. A knowledge of the properties of one plant is a guide to the practitioner, which enables him to substitute with confidence some other that is naturally allied to it; and physicians, on foreign stations, may direct their inquiries, not empirically, but upon fixed principles, into the qualities of the medicinal plants which nature has provided in every region for the alleviation of the maladies peculiar to it. To horticulturists it is not less important: the propagation or cultivation of one plant is frequently applicable to all its kindred; the habits of one species in an order will often be those of the rest; many a gardener might have escaped the pain of a poisoned limb, had he been acquainted with Natural affinity; and, finally, the phenomena of grafting, that curious operation, which is one of the grand features of distinction between the animal and vegetable kingdoms, and the success of which is wholly controlled by ties of blood, can only be understood by the student of the Natural System. [John Lindley, A Natural System of Botany, Longman et al. 1836, viii]
This is almost exactly the justification of phylogenetic analyses, contrary to those who think that there is something else important about them, like history or technique.