Question

Why are archaea in a separate domain from bacteria apex?

Answer 1

 They are thought to have different paths of evolutionary development.

Answer 2

I believe this is because Archaea differ from bacteria in a number of ways. These includes;
Unlike bacteria, archaea cell walls do not contain peptidoglycan, Archaea have different membrane lipid bonding compared to Bacteria and Eucarya. That is Archaeal lipids lack the fatty acids found in Bacteria and Eukaryotes and instead have side chanis composed of repeating units of isoprene. Other differences are like Bacteria, Archaea have 70 S ribosomes, but they have a different shape; Archaea have more complex RNA polymerases than Bacteria, similar to Eucarya.