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I agree with Alistair, but I also wondered if it had something to do with the parents. When he got his acceptance letter, his parents seemed mostly worried (at least the dad did, from memory), and now after partially learning about his past it makes me think that he was mainly reluctant to have Simon attend the academy at all.
Maybe he thought "if I don't teach him anything, the academy won't admit him since he won't *have* a talent in anything."
Still, as parents with immense talent (both mom and dad), and knowing how much they're being monitored by the empire because of they're background, it would have been a better idea to properly equip Simon and teach him anyways. At LEAST the basics of the basics!
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And Simon being ranked as #1 despite currently lacking skills for it, could be due to nepotism, yeah, but also to keep a closer eye on his growth or it could be based on over-all potential.
Like, he kinda sucks now, but he has the most potential of all the top ranked students to be the most powerful.
Honestly, it's probably a mixture of all of that.
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I mean even now he doesn't even really suck he just lacks the basics.look at how after one lesson on how to control skeletons and how to control the bones how much he advanced. If he had done the prep everyone else had done there would be no question on whether or not he would be #1.
Also re reading it I think your right about his dad not wanting him to go. I think they assumed if his background got exposed he might be discriminated .because of his mother. But since he got in because of the headmaster they felt more safe in letting him go because she would have his back?
I have read quite a few necromancer manga, I have never seen them trying to reassmble a skeleton because usually when you use your necromancy power they are already assemble. I thought that's what this was going to be like but it's not.
I find it weird that the MC got the Special Admission Number 1 when he didn't even learn anything. Why did his father not teach him anything until he was accepted in the school and he only taught him about the darkness power and that's it. Since his father should of known what the academy was like since he as been there himself. He never taught him anything about it. Most of the students actually had prep courses.