I am not sure to be within the topic of this site but I can't figure out where would be better? Maybe on linguistics.SE but not sure either so I post here. If you feel this is too broad a question, I will not take any offense if you want to see it closed but the problem I want to draw to the attention to is a problem that, I think, is experienced by a lot of people.
Even though this is not a problem where only the Japanese language is concerned, I think it is a problem that is exarcerbated when trying to improve in Japanese or a language far from one's native language.
Most of the very actively spoken languages are from the Indo-European family which make them more easy to grasp because there are some deep underlying similarities like word order which is mostly preserved. But when it comes to other languages with no apparent common points (Arabic, Japanese, Korean, Siamese or the like), the new learner is left with almost no points of reference and it is like restarting from scratch.
Restarting from scratch is not a problem itself, but it can't be achieved with no bias from one's previous knowledge. When you start learning a new language, you will do it form a language you already know. In the best case, you already know a handful of languages (not really likely but well), you will try to learn a new language from a language that is similar. For example, learning French from Italian, German from English, Finnish from German, Korean from Japanese. But most of the time, one does not have such possibilities and will end up learning a new language from its native language.
Learning a language from one's native language seems at first glance very convinient because it will give you the illusion that you perceive every nuance to the best since you can express it the way you like in the language you are the most used to. But it is kind of a double edged-bladed with sharp edges. Eventually, you will end up thinking in you native language and translating to your target language or translating (almost unbestknown to you) from your target language to your native language because this is a necessary means to your understanding.
One way to solve this problem is to use the direct method. Learning the language from the language, it may seem tantalizing but is it really? There is no textbooks/whatever that use this method. One can argue that the Minna no Nihongo series is an implementation of the direct method but I do not think so. This book series can't be done with a teacher and often (most of time/always) the book will be explained in the native language of the course's attendents.
Another paliative method to the direct method is when one's level is high enough, one can switch is language studies to the language he/she is studying. (But there is still the risk that internal tranlating occurs)
Let's now come to the point of the topic, naturalness. Naturalness is speaking like everyone do. Do to so, a textbook is of pretty much no use. What is needed is exposure. Well, but what kind of exposure? Reading a lot is of no avail, listening a lot is pretty much the same (because of internal translating I mentionned above). Nevertheless, it should be granted that reading/listening will definively help you knowing what is natural from what is not. But at the same it can be misleading (the language that can be found in manga is not recommended to use for real life communication for example). Nevertheless, what is good is that in general what you are reading/listening is produced by native speakers and as such natural.
In order to improve naturalness, it seems that input can't be everything, output too is as much as important if not more. Output basically consist of talking and writing, but with who? You can effectively talk to you (good to improve charisma), with your class/roommates, parents, whoever who is learning the language and who is not remotely far. But that's far from being good either for you and for your interlocutor since you may influence eachothers will end up saying totally wrong things (you will understand yourselves but any other one will not understand).
Speaking with native speakers may as well be a solution but most of the time, as long as they understand you they won't point out your mistakes because it is tedious and they do not want to be troublesome and may want to avoid troublesome questions from you as well. (Children get more easily corrected than adults because they are going to school and they will get corrected (sometimes harshly) by their teachers since that is theirs trades.)
Therefore, two questions emerges from this:
- Is it possible to achieve naturalness, then how?
- Is it possible to disable the proccess of (internal translating to one's native language)?