I think there is no taxonomic system that could resist changes over time.
There might be a robust taxonomic system that is not liable for the change in the short term.
In-plant systematics (for example), the phylogenetic classification is now widely used. But, a clever taxonomist couldn't ignore to merge between this cutting-edge technology (molecular phylogeny), and classic taxonomy (morphology, anatomy, and karyotyping, etc.)
If I get the question right, you are looking for an absolute method to use in taxonomy. There is no absolute method in taxonomy, but the most recently used projection in this field is Integrative Taxonomy: This uses tools from other fields, just like Ecology, Evolution, Ethology, Phylogenetic, Morphometrics, etc, together these allow a more exact approximation, to define a species and its systematic.