Possible rationales that taxonomists might have used when deciding to group prokaryotes into two distinct domains instead of in one group

For a long time, there was only one group of prokaryotes that was recognized by the scientific community, the bacteria. But, with the development of the methods of molecular biology and genetics, it became evident that the archaea are quite different than bacteria and should be regarded as a separate domain.
Even though they are both prokaryotes, lacking the organelles in the cell, the structure of the membrane of archaea is different from both the bacteria and the eukaryotes. Furthermore, analysis of the genomes of the 3 domains proved that the archaea are truly a separate group, having some genetic similarities with both eukaryotes and the bacteria.

Oh dog