Keep in mind that Waffle said cutest. Since Flandre is often portrayed with creepy qualities, she doesn't qualify as much as Sophia. (Plus I don't think Waffle likes the ones that are already psychotic to begin with, as his fanfics imply.)
Technically, Flandre was never psychotic, from what I remember. It's only the fans' interpretation that she is.
Sorta like how Tenshi is Masochist, when she's really not. Or maybe that Cirno is the physical manifestation of the number nine, and nines are idiots, when Cirno's just innocently unaware to her surroundings.
The Touhou series is weird like that, since ZUN, the creator, allows fan stuff to be "official" interpretations. That's why there's so much Touhou related stuff out there. ZUN doesn't try to stop the fans, but rather encourages it. Touhou is technically public domain, but don't quote me on that.
But yeah, Flandre didn't really go mad from 495 years in imprisonment, but rather she's sheltered from not knowing the outside world. She has the power to annihilate the entire dimension of Gensoko (the dimension Touhou takes place in) with just her right palm, so maybe that's where her insane qualities came from.
Or maybe it's because she doesn't know the meaning of pain nor death, so she tortures her opponents without realizing.
Or maybe she's just crazy powerful.