The definition of species and for the matter, taxonomy in general should be tied to a purpose other than the classification of organisms. We do not classify organisms simply because we want to classify organisms, we classify them because we want to use that classification for some purpose. For example taxonomy generally involves areas of interest (can they mate, can they live in a certain ecological environment, can they produce certain biological products, can they fulfill certain biological roles etc.) tied to recognizable markers (if an organism has these markers, it will then possess the traits/abilities of interest). Each taxonomic rank basically uses a set of markers to further divide groups of organisms, with every rank down using more markers.
Perhaps the species level should be more fluid, accommodating a variety of markers, each specific to its area of interest, and "species" replaced by a variety of terms with each term representing a different set of markers.
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