Koishi was actually the.... maybe the third or fourth extra I beat?
But the reason I say she's high up is because she has a lot of spells that aren't those "figure out the gimmick and then it's easy" types I was just talking about. There are no tricks or routes for Id, Ego, Embers of Love, or Rorschach, you just have to be good enough to dodge them. Routing certainly makes Youkai Polygraph and Genetics easier, but routes aren't enough to beat them the way they're enough to beat Suwako or Flandre's survivals.
Her patterns aren't exactly easy to read either, the way, say, Danmaku Chimera is. Every extra boss has 1 or 2 patterns like that (Charming Siege, Froggy Braves the Wind and Rain, Apollo Reflection Mirror, as some examples) it's just the fact that Koishi has a lot. Raiko and Mamizou also have quite a few, which is why I said they were higher up.
I'm also saying this relative to their respective games. Hecatia is the hardest extra boss imo, but by LoLK standards she's not that ridiculous.