A number of reasons.
For starters, he's unique for JoJo villains.
While Dio, Kars, Pucci and the rest who all have these grandiose plans like becoming some all power god being and ruling the world, Kira's primary goal is as simple as wanting to enjoy his sick little twisted life without anyone hindering his habits. He's not after supreme power, or immortality, or ruling over heaven, or making America great again. He just wants to continue living quietly with his dark secret life intact.
Another reason is how decidedly simple his stand is.
While everyone else has stands with an array of flashy or complicated effects...Killer Queen just makes shit explode. At least until Bites The Dust. It's so decidedly simple in a universe filled with absolutely silly and nonsensical powers.
The lengths that this hypocritical manchild with too much power goes to just to keep his favorite pastime a secret affair is mind boggling, and the fact that he can blend in so perfectly and seem so completely normal and mundane while being the most unhinged villain throughout JoJo makes him stand out.
Plus he's just so...Completely fucking absurd, even by JoJo standards, once his calm and collected personality starts to deteriorate throughout DiU when he realizes that an increasing number of people have picked up his scent, and the paranoia starts settling in.
And a character like that would stand out more in a cape-shit comic (Especially against someone like Batman or The Question) which already has countless ambitious strongmen vying for power like Dio, or corrupt and powerful politicians bent on consolidating their power like Valentine, and even "An ancient evil has awoken" monsters like The Pillar Men.
Kira would basically be The Joker, if The Joker had no desire to grandstand, left behind virtually no trail, and could perfectly blend into civilized society.