Dear God, I think you may have provided the insight to understanding this whole thing. First of all, let me say that your post closely mirrors a review written contrasting Will and Clarice's characters.

http://nickyarborough.com/the-manhunters-will-graham-and-clarice-starling/

The relevant quote in your reply is as follows:

Clarice as she was in the movie, is a fantastic opposite of Hannibal. She has a keen sense of justice. She's determined and genuine. She will go to the darkest of places to save whoever she can and still remain untainted by it. I think she can understand Hannibal without becoming Hannibal which sets her apart from Will.

I think this may be it exactly, and the driving gears in the clockwork that would then form the resolution of this grand odyssey Fuller is embarking us all on. Clarice is different from Will in this regard--and I had admittedly never considered it before you said it. The FBI agent who expressed an aura of innocence: that always was Clarice Starling. She had inner strength--tremendous--but was soft and gentle and entirely fueled by morals. More like a Joan of Arc figure--Whereas Will could double as a light version of Hannibal Lecter, Clarice truly is his opposite.

And that fully and honestly is what attracted the monster's attention.

Now I feel I suddenly may perceive where Fuller and Co are taking this, and if I am right...It's actually fantastic, and I definitely spoke too soon. After googling this inquiry, Fuller seems to have indicated that the last season of Hannibal (Number 7, if we're lucky), will be original content set after the canon literature. That would set us directly post the events of the novel Hannibal--and what we know it entailed. Quoting from your post, "It's pretty retarded how she ends up in the books", Yeah, it is. Once again, spoilers ahead, but I don't think anyone discussing on this thread doesn't already know the ending anyway. Clarice doesn't exactly just run off with Hannibal into the sunset. He drugs, hypnotizes, and then brainwashes her. It's heavily implied by the end of the novel, that she is still in a state of hypnosis--recall that particular musical note she has to hear in order for "awakening" to occur?

Enter the ingenious conclusion of Hannibal the TV show, if this is the writers' intention for the storyline. When Lecter meets Clarice, he is fascinated by her goodness and innocence, notwithstanding the fact that he is a cannabalistic serial killer. Reflecting on the way the television show portrays Hannibal Lecter's madness, I'm not sure that's actually too far-fetched. Lecter can be evil himself but still embrace a philosophical side about humanity which he uses to find beauty in the world. Clarice Starling's morality is what makes her beautiful; in the SotL film, we already saw him sketching drawings of her, as though he were depicting her like a saint. Hannibal never attempts to persuade Clarice to choose him, as he did Will; he already knows the tone will fall on totally deaf ears. The brainwashing of Clarice Starling is a given, or else zero chance exists of her tolerating his companionship. Granted, in the books, his original aim was to reincarnate Mischa, but the practical ease that shows Starling overturn that grain in his psyche can rightly be interpreted as evidence that a strong, underlying attraction was always existant. In the novels, Hannibal Lecter accepts Clarice as his lover, and it would seem is totally satisfied with such a state of affairs, albeit forgetting about Mischa. The monster, in other words, appears to actually get his happy ending...

But not all are happy. Will Graham, the former FBI agent who has been in retirement ever since the events of Red Dragon, gets wind of this development from Jack, and finally erupts out from his reduced psyche of misery and alcoholic depression--he is not going to let Lecter win this one. Lecter murdered Abigail and/or Alanna (waiting on Season 3 revelations), destroyed his marriage and family life with Molly, and ruined both his body and mental state: he is not going to ravage a good and independent spirit like Clarice Starling from the world. And so, for Season 7 and the conclusion of the televised Hannibal, the stage is set: It's the pursuit of Hannibal and the reclamation of Clarice. Will Graham thinks he's the only one who can crawl inside Hannibal's mind and foreshadow his whims and maneuvers; Jack Crawford is driven by personal vendetta, swearing that this will not be a repeat of Miriam Lass; Hannibal is ready to kill them in the blink of an eye if they threaten to take his plaything away from him and poised to mock them from the shadows--for as stated in Season 2, it is difficult to catch a fish once it's gotten away a first time; and the wild card in the deck, Clarice Starling is actually on Hannibal's side...

This would totally fix the screwed-up ending that was the novel Hannibal's conclusion, and equally maintain the focus on Will and Hannibal's relationship that is the theme of the TV show. It would draw the outline for the ultimate showdown. I hope now that the writers do take it in this direction and that we get to see this climax of things--sampling his imagination up to this point, I tend to think Bryan Fuller and Co would do it justice.