Always been there either through costumes or characterisations, but if they had a good story, they normally didn't focus too much on the sex sells:

• Sailor Moon (tiny skirts, and there is a 14 year old girl who had a relationship with an adult male who is a demon)

• Gurren Lagaan: Look up "Yoko Littner", she's 14.

• Tokyo Mew Mew (Mint has a really short mini dress)

• Higurashi no naku koro ni: One of the special episodes features a scene where one of the highschool aged characters are naked on the table with sushi all over her body (nyotaimori), the context was everyone was discussing penalties to losing an innocent game I think and they were imagining.

• Clannad visual novel game (love interest looks like a little kid and acts like a little kid, she's older than the protagonist and is repeating her final year in highschool)

• Ore no Imōto ga Konna ni Kawaii Wake ga Nai light novel series (2008): Older brother loves little sister

I watched the anime adaptation of some of these and read the manga originals or adaptation. I remember they were very popular or popular enough to recieve an anime adaptation and to be exported to English speaking countries. It probably increased these days, it's getting harder to earn more as a mangaka (manga author) or an animator. Almost all of the time, it's fanservice. I read somewhere that the "little sister" trope is popular because majority of Japanese males are only-child and they like the whole "being dependable" thing. Also Japanese culture as a whole is really misogynistic and also does not foster socialisation that well (I think mainly in the city areas, I'm not so sure about the rural areas) so many people, from child to adult don't really socialise and feel confident about approaching another person because they spend all of their time studying. I could be wrong though, it's based from what I read up.

Your post does make me question if there's a link between trans people and gsming (specifically, the Sonic series), but really it boils down to them enjoying an attractive accessible medium. Manga style is attractive compared to other styles because of the level of semi-realism a person is often drawn in that format, comlared to American cartoon styles (e.g. Simpsons) and have softer lines and colouration compared to American comics (e.g. DC). The style looks easier to draw compared to American comics. That's my theory though. Part of it is why I like manga drawings over American style comic drawings.