Fun fact: this is Ruby's voice actress favorite ship.

Neh man, the only think people making doujins are catering to their "onee-chan lolicon rape fetish" with Shirou.
People actually don't make any yuri doujins because they don't need it, it's already everywhere in the show. (they prefer to make doujins with Shirou to satisfy their 'lolicons needs')
And even though Illya and Miyu have an obvious Nanoha/Fate relationship, Kuro is so tsun-tsun for Illya in the second half of 2wei (especially in the manga) and so overprotective of her in 3rei that it's obvious she has started to fall for her as well.
The 3 of them form the best yuri triangle ever.

There's far more chemistry between Illya and Kuro than with Miyu.
Kuro went from only wanting to kill Illya and take her place, to become her overprotective 'big sister'.
And Illya went from wanting Kuro to just disappear from her life, to wanting them to never be separated ever again.
Miyu can be the third wheel, since their relationship hasn't changed in 4 seasons...