Dear Mrs Authoress,
There was a delightful exchange between a playwright and Conan Doyle: Q: “May I marry Holmes?” A: “You may marry Holmes, murder him, or do whatever you like to him.”
May I just say, now that you want to play playwright rather than Doyle, that no, you got it right the first time? To say that, as the story played out, it isn't about Potter, (Potter is central to the unfolding, but it's not about him) but about families: that the first big thing we do after Dumbledore's funeral is throw a wedding; that what saves the Malfoys is they decide not to be soldiers anymore but again a family; that Riddle was ruined because his family (mother included) ruined him, just in time for him to destroy them. (Potter doesn't turn into a Dursley, because the Dursleys themselves were scrupulous about keeping Potter out.)
And so, if the story must extend to the generation that follows (it needn't, of course, but that is what happens next) and if that is a happy ending, then the sympathetic characters (Ok, maybe Potter isn't so sympathetic anymore) ought to be well-matched for the purpose of being family. Potter, alas, has grown up without his proper, visible, natural family, and he doesn't connect at all with Hermione's family (they sort-of paper the walls of Diagon Alley once or twice, I think); indeed, who, in the whole tale, knows enough of the running of a family to supply what is wanting in Potter's experience, and can marry Harry and already loves him? I submit that only Ginevra will do.
Leah Libresco very sensibly acclaims the platonic love (I'd say philia) between Harry and Hermione; and why throw away that beautiful moment when Ron himself destroys a bit of Riddle's evil?
I am sorry to hear that you, the immediate author of the original tales, have twice now, been more than willing to recast your characters along lines of will and power, twice now in connection with the generative power and its degenerations. Go read some Tolkien letters (at least when he revises a story, he makes it better), and play with your children some!