I've found my people.
Throwing my two cents into this, I'd say that it mainly deals with how many times characters appear whether it be in canon or fanworks. Characters like Sakuya and Aya have been around for around 20ish years, so they've had plenty of time to permeate throughout the series. I think a big reason why people like them is simply because they can associate them with more content than other characters like Rika who have been around for longer but have not gotten much love from the source material or the community. Using Sakuya as an example again, she has been playable in a few mainline games, has plenty of remixes of her themes, an endless amount of fanart, plenty of fangames, etc. I can't remember the last time I have seen fanart for a character like Riko that I didn't go out of my way to look for.