Frankly, this is one of your worst stories. You're a very good worldbuilder, but you're not very good at writing romantic relationships.
Hermione, in the books, is a perfectly normal girl. She is probably more intelligent than most people her age, but still normal. You have, using the excuse that she is Harry's soul mate/one true love, turned her into the most beautiful/intelligent woman in the world, a perfect goddess that can do no wrong. In other words, you've turned her into a Mary Sue. The Heir-Of-Everything/Superpowered Harry is also a bit of a Gary-Stu, but he was much more bearable than Hermione. The relationship between them was very forced. I think the fic would have been better if you kept the Harry/Hermione romance to the side.