There are 2 Naruto trainer games on this forum if you have not seen them. Sadly they are both early in development.
I got to say, anime is pretty popular subject matter for hentai games. Just off the top of my head, I can mention zone (kill la kill, ghost in the shell, many many more)
Of course they are all flash games, and may not be the sort of visual novel you are looking for. In that case you do have a real problem though, which stems from the fact that creating adult games is a real business in Japan, which automatically makes it impossible to sell and market games like this without infringing copyrights. The only reason Akabur's witch trainer or mitty's elements trainer are immune, is because you are not paying for the products, but you are supporting the artist through patreon, who then in turn rewards you with a product. It is a clever way to circumvent copyright law, something that the Japanese are yet to embrace entirely.
I too would like to see highly developed games based on anime franchises, but lets not despair entirely, a major bulk of all existing hentai is based on anime, you just have to accept it in flash games or comics/pictures.