To demonstrate you are an independent researcher, you should choose methodology correctly and explain why these methods are most appropriate for your research. There are inductive and deductive methods of exploring your field of study. Inductive methods give you an opportunity to collect data on the investigated topic and, after that, to formulate theoretical assumptions on the basis of the collected information. The deductive method leads you from theoretical assumptions formulated by you or by others to practice. The main sign of your independence as a researcher is your ability to prove the correctness of the chosen methods and demonstrate that you know how to combine them.
Another purpose of a doctoral research is to show that its author belongs to the modern academic culture. In other words, this person follows all the instructions accepted in this culture. An academic discourse is a tradition that has been established for the last two centuries. The modern rules of writing academic texts emerged in the 19th century. For example, David Hume did not use references and footnotes in his writings and was criticized by his readers for that. He answered his critics that using footnotes was not typical for his outstanding predecessors. Thus, the doctoral research shows that you know and agree with the requirements of the modern academic culture.
It is difficult to be the first, but the purpose of a doctoral research is to discover or to investigate a new segment of the field that is under-investigated or totally unknown. To prove you are a pioneer, you should demonstrate your acquaintance with the primary and secondary sources on your topic and your profound knowledge of them.
It is known that any epoch in the history of science dictates its main paradigm to the researchers and imposes particular rules and perspectives on them. Our epoch is more tolerant to perspectives' diversity, hence, you should demonstrate in your doctoral research different perspectives on the subject under investigation and to explain why you have chosen a particular perspective as a dominating one.
The main purpose of your doctoral research is to prove to experts in your academic field that you have deepened the knowledge about the subject. Show that your contribution helps in solving particular scientific problems. Demonstrate how your findings can be applied to practical tasks. Generally, any doctoral research must have practically applied results.