Personally, I'm actually quite fond of them, especially for anime continuua (that is the proper plural of continuum, isn't it? If not, I apologize). Depending on the story, the characters might still retain whatever superpowers/odd physical traits they had in canon, or still have part of them, or have nothing but the name. These last make me sad, but oh well. Moving on.

Killing them is both easy and not, I would imagine. (All of this is hypothetical, mind, since my agents a) aren't assassins, and b) have never worked in an AU before. Actually, for that matter, they've never worked anywhere, officially. I've been slacking on the writing of their missions. But that's completely off topic.) Most AUs are set in what can be assumed to be World 1, so you have access to all of the World 1 weapons. On the other hand, getting guns etc. into High School isn't terribly easy, and they tend to be chock-full of OCs who would notice. I'd say if you had something subtle like a curare-tipped blow dart, it might be the most effective. Killing someone in math class is surely fun, though charging them in class might be a bit disrespectful to the teacher.

--anamia

Every new thread you make pushes another off the front page, and another at the very back off into oblivion. With your three threads you've already shoved another three off in a short period of time.

If you have any more questions or ideas, mind keeping them to one of these threads that you've already made for now?

Otherwise you're crowding others off of the first page, and hardly anyone goes back farther than this one.

If you're dealing with a continuum that has mecha as very commonplace, you may be able to use a disguise that will be able to deal with your sue or possessed canons. If not, you'll have to use a disguise that's normal for that continuum, and get creative. It's almost always preferable to disable powerful Sues by stealth and trickery rather than trying to fight them outright. Sometimes you can wait for a part of the fic where they're hurt or unconscious and capture them then.

I don't like High school AUs, but they're a well known fanfic genre, and good ones (presumably) exist. They are written with three basic rules in mind:
1. The characters have grown up in a modern world.
2. The characters are all the same age--namely, teenagers.
3. The characters are all attending high school.

Like any AU, the issues aren't with the changes that make it AU, but with not fully exploring the results of those changes, with general bad writing, and with creating unrealistic, implausible situations that are meant to do no more than set up a favorite pairing.

Pulling the characters out of character in any way that couldn't be justified by having them grow up as, and be, modern high school students is still bad writing. You will often find that a Mary sue is at the center of the plot, either a sue version of a canon character or an OC.