Here is my theory (springing from the aside in the last entry):

At one point, the heroine of Pumpkin Scissors has to finally grit her teeth and meet her arranged fiancee. There's a lot of ways this could go badly for her, but actually he's a cool guy; he's nice, competent, powerful, understanding, and of course it turns out that he's one of the lead villains. How predictable.

But let's think of it from the other side. From a story perspective, how do you keep her fiancee from taking over the show given that he's a secondary character?

Roughly, I think that there are three main things that you can do in this situation:

• Somehow sweep the secondary character more or less off stage. This both wastes the character (why introduce them at all if you're going to make them disappear) and is unrealistic in this sort of situation; the better they are the harder you have to work to make them disappear.

  (This works best when you have a clear reason for why the secondary characters are secondary and can't become part of the protagonist team.)

• Bite the bullet and have them become part of the protagonist team. There are all sorts of drawbacks to this, especially if the secondary character is (very) competent; the more flawless they are the more they dominate the real protagonists (and the less interesting they are), and the more flawed they are the more time you spend exploring their flaws instead of dealing with the actual protagonists. This is where they take over your show.

• Make them villains, thereby making them part of the main plots without detracting from the protagonists.

  (In theory you don't have to make them literal villains, just people who oppose the protagonists in some plot-relevant way. In practice I think that making them villains simplifies the story in a bunch of useful ways.)

Another way to put this is that unless you have an unusually long anime, you probably don't have much time to deal with things that don't involve the main plots. This implies that secondary characters have to either help move the main plots forward or not be around very much, and there are a limited number of ways they can move the main plots forward. If you need villains, it must be tempting to (re)use a character you need to have around anyways; it kills several birds with one stone.

(Also, you probably only have room for so many characters before your audience gets lost in the cast. If you only have room for ten major characters, you have to make all of the significant roles you need filled fit into those ten characters. If you need a romantic rival and a villain, well, maybe you can combine those together to save space.)