I'll give it a rating of 5, as it's really good for fan fiction. But I can't call it really good, because there are several significant flaws that leave a bad aftertaste:
1 Mary Sue characters. Well, just classic - very strong, very smart, very handsome. And if in such a Tom can still be believed, in the presence of an incredibly powerful witch from an ancient family with an incredible mind - no. The whole plot is essentially built on the awesomeness of the second character, and the others are scenery for him.
2 There is no confirmation of the characters' incredible intelligence. The main character doesn't have a single plot twist that shows her genius. Only descriptions and praise from other characters about her intelligence. No really interesting and outstanding solutions, assumptions, etc. she puts forward. An ordinary girl by deeds, but completely unbelievable by description and by what Tom thinks of her. And it's all just in the descriptions. And we have to believe it.
3 Tom isn't bad, but again, his psychopathy and incredible intelligence don't fit in any way with many of his irrational actions. I just don't believe it.
4 Despite the author's beautiful writing style, the descriptions are tiring - the same thing sometimes in the same words. Many times it is said how incredibly beautiful Tom, how incredibly smart Varya and how incredibly evil they are.
5 A dragged-out ending and basically a drag on the text with descriptions.
6 Logical lapses in the plot. For example, about Varya's power, etc., about her ability to control her, death. Not fully properly explained and justified.
7 Ending. I have very big questions about Tom's cowardice and his fear of admitting his feelings. First, questions to the fact that he has them at all, and second, while he has them, these mental tossings of his 15 chapters truly look tiresome. It would have been much more beautiful for him to be honest at least at the end, but to remain true to his ways. As it is, it looks like a failed puberty.
On the plus side:
1 There's no quick and dumb relationship development, Tom stays partly true to himself, though the rationale for their relationship isn't believable either. There is nothing that would make such a Tom by description fall in love with Varya: there is nothing in her actions that can really be called the most brilliant and powerful, one is only invited to believe the author. But nevertheless, I'm glad that Tom didn't turn into a total sniveling snot until the very end.
2 There are interesting plot twists, I was especially moved about the Death Eaters.
3 Despite the Mary Sue of almost all the characters, the characters still try not to be so flat, there is some liveliness in them, although they remain essentially only scenery.
4 The development of the relationships is still exciting, you want to know how it all ends.
All in all, I would have given it a 3 if I were judging it as a work, but for a fanfic it's a 5.