Thank you for the opportunity to help you with your question!
The 5 kingdom system used cell morphology to classify which was not so acurate, The 3 Domain system uses S r RNA gene to differentiate organisms. This is important in suport of a similar origin and changes emanating at change at gene level.
It makes more sense as each of the three cells tends to fit into reccuring specialities and role,e.g bacteria tend to be the most prolific producer.
Please let me know if you need any clarification. I'm always happy to answer your questions.