What the Ministry of Justice website says about naturalization

It doesn't say much. It basically says that naturalization is a non-trivial procedure, and the papers you need vary per person and you should make an appointment to talk with them directly.

This is what their only webpage looks like:

トップページ { toppu pēji} → 行政手続の案内 {gyōsei tetsuzuki no annai} → 国籍関係手続 {kokuseki kankei tetsuduki} → 帰化許可申請 {kika kyoka shinsei}

帰化許可申請 {kika kyoka shinsei} (Applying for Permission to Naturalize)

手続名 {tetsuzuki-mei} (Procedure Name)	帰化許可申請 {kika kyoka shinsei} (Applying for Permission to Naturalize)
手続根拠 {tetsuzuki konkyo} (Procedure Foundation)	国籍法第４条第２項 {kokusekihō dai-yon-jō dai-ni-kō} (Nationality Law, Article 4 Paragraph 2)
手続対象者 {tetsuzuki taishō sha} (Procedure Applies to)	日本に帰化しようとする外国人 {nihon ni kika shiyō to suru gaikokujin} (Aliens attempting to naturalize to Japan)
提出時期 {teishutsu kikan} (Submission Period)	随意 {zuii} (Voluntary)
提出方法 {teishutsu hōhō} (Submission Method)	帰化しようとする者が１５歳以上のときは本人が， {kika shiyō to suru mono ga jūgo-sai ijō no toki wa honnin ga,}１５歳未満のときは親権者， {jūgo-sai miman no toki wa shinkensha,}}​後見人などの法定代理人が， { {kōkennin nado no hōteidairinin ga,}​法務局又は地方法務局に自ら出頭して， {hōmukyoku mata wa chihōhōmukyoku ni mizukara shuttō shite,}書面によってしなければなりません。 {shomen ni yotte shinakereba narimasen.} (In person if the applicant is 15 years of age or older. For those under 15, one’s parent or legal guardian or legal representative must be present depending on the documents.)
手数料 {tesūryō} (Handling Fee)	手数料はかかりません。 {tesūryō wa kakarimasen.} (There is no handling fee.)
添付書類・部数 {tempu shorui · busū} (Documents Needed / Number of Copies)	個人によって必要書類が異なりますので， {kojin ni yotte hitsuyō shorui ga kotonarimasu node,}​申請を行おうとする法務局又は {shinsei o okonaō to suru hōmukyoku mata wa​地方法務局に相談してください。 {chihō hōmukyoku ni sōdan shite kudasai.} (The number of documents depends on the individual, so please consult with the main or regional Bureau of Legal Affairs.)
申請書様式 {shinseisho yōshiki} (Application Form Formats)	申請書は， {shinseisho wa,}提出先に備え付けています。 {teishutsu-saki ni sonoetsukete imasu.}申請書以外にも種々の書類を提出する必要がありますし， {shinseisho igai nimo kusagusa no shorui o teishutsu suru hitsuyō ga arimasu shi,}​申請書類が揃っていれば必ず許可されるものではありませんので， {shinsei shorui ga sorotte ireba kanarazu kyoka sareru mono dewa arimasen node,}​申請を行おうとする場合は， {shinsei o okonaō to suru baai wa,}​事前に申請を行おうとする法務局又は {jizen ni shinsei o okonaō to suru hōmukyoku mata wa}​地方法務局に相談してください。 {chihō hōmukyoku ni sōdan shite kudasai.} (The written application will be provided at the place of submission. In addition to the application form itself, many other documents will be required and must be presented at the time of application in a full set and there’s no guarantee that you’ll receive permission even if you complete all the paperwork, so before submitting please consult with the main or regional Bureau of Legal Affairs.)
記載要領・記載例 {kisai yōryō · kisairei} (Sample Application Forms)	別紙のとおり。 {besshi no tōri}なお具体的には， {nao gutaiteki ni wa,}申請を行おうとする法務局又は {shinsei o okonaō to suru hōmukyoku mata wa}​地方法務局に相談してください。 {chihō hōmukyoku ni sōdan shite kudasai.} (Attached here. For specific details, please consult with the main or regional Bureau of Legal Affairs where you intend to apply.)
提出先 {teishutsu-saki} (Where to Submit)	帰化申請をしようとする者の住所地を {kika shinsei o shiyō to suru mono no jūshochi o}​管轄する法務局又は地方法務局 {kankatsu suru hōmukyoku mata wa chihō hōmukyoku}​（国籍事務取扱支局を含む） {kokuseki jimu toriatsukai shikyoku} (The main or regional Bureau of Legal Affairs — that has a Nationality Section — which has jurisdiction over the naturalization applicant’s address.)
受付時間 {uketsuke jikan} (Hours of Operation)	提出先に確認してください。 {teishutsu-saki ni kakunin shite kudasai.} (Please confirm at place of submission.)
相談窓口 {sōdan madoguchi} (Consultation Location)	提出先 {teishutsu-saki} (At place of submission)
審査基準 {shinsa kijun} (Examination Standards)	ありません。 {arimasen.} (None.)
標準処理期間 {hyōjun shori kikan} (Standard Processing Time)	ありません。 {arimasen.} (None.)
不服申立方法 {fufuku mōshitate hōhō} (Methods for filing a complaint)	ありません。 {arimasen.} (None.)

I'd like to think that the handling fee is ¥0 is because there're trying to increase the population through immigration, but this can't be the case because there has never been a fee as far as I can tell. Considering the amount of labor and processing that naturalization takes, and considering the fact that you get a dedicated case worker to guide you through the process, this is not a bad deal.

Notice the "apply in person" phrases. While you may decide to hire a service to prepare and translate your paperwork for you, you're still going to need to show up in person for many of the steps. (and your "motive for naturalization" paper needs to be in your own handwriting (no word processing or translating), in Japanese.

The MoJ site points to two example applications. One application is taken straight from the 28 page guidebook, documenting a fictional Korean national that naturalized. The other document, though, is for somebody under 15. That example is not in my guidebook. Perhaps there's another guidebook detailing the procedure for children. If there is, I don't have it.

The hours of operation row, in English, means "by appointment only."

Although there is no "Standard Processing Time," my case worker did say, given no problems, the process should take eight months. Possibly longer than a year if issues arise, he warned.

The lack of "Examination Standards" means that there is no magic (known) formula for getting naturalized. Even though the framework (the six requirements is known), the exact level of Japanese, the exact level of income per person, etc., is not set in stone.

And finally, the last row (Methods for filing a complaint) means that if you are rejected or have a bad experience, there's no formal appeal process. There is nothing stopping you, however, from applying again.