It might be because she felt very shoehorned in, in FireRed and LeafGreen, and that they were very unpopular games in general.
Kris is known because Crystal was a popular game, May is popular because RSE were generally well-liked games, and Dawn was... I'm not sure, I don't personally like Dawn, but she was also pretty popular, but by then, we'd accepted that every Pokémon game would have a "boy" option and a "girl" option.
When FireRed and LeafGreen came out, they were ultimately very disappointing games, with a lot of people ending up hating all the elements they introduced (of which, there weren't many) - and I suppose that's why Leaf often gets overlooked. If she had been introduced in Gen 1, or featured in the anime early on, etc. then she'd probably be the most well liked female playable character.
Her design is okay, nothing special. She's not really the focus of any other media, aside from having a vague counterpart in the PokéSpecial manga. She was never in the anime, like Dawn, May, or XY girl.
So the odds have always been stacked against her.
