People are tools. People are stupid and easy to manipulate, and, more importantly, people are delicious when handled properly. Will Graham is nothing like the people that Hannibal is used to dealing with. Not even Bedelia, who simultaneously seems to know too much and nothing at all.
Hannibal prefers to surround himself with interesting people. Will and Bedelia are his favorites. Beverly Katz also seems to have a trickle of potential, but it's not nearly enough. Jack Crawford is of less intellect than a schoolyard bully despite his position in the FBI and his occasional moments of wit (such as hiring Will Graham, perhaps). Freddie Lounds is smart and remarkably manipulative, but Hannibal finds her too irritating to care about her. Abigail Hobbs knew too much. Anyone else has hardly caught a sliver of his attention.
Will is of one major flaw, however. His work leads him far too close to Hannibal's true self. This could be interesting, but Will Graham is dead set on sending the murderer to jail, and Hannibal can't have that. So, when Will figures it all out, Hannibal frames him. He doesn't want to, but it's a necessary evil.
The point of sending Will to jail is not to get him out of the way, nor to keep him there. The point of sending Will to jail is to keep him away from his friends at the FBI for long enough to convince him that Hannibal is not to blame for the murders. Once that is accomplished, Hannibal will let him out of jail. And Will does believe, after a while, that he was wrong. His trial will have to go well.
It doesn't. Hannibal will not stand for this. He considers killing Will's lawyer, but he figures that that will achieve nothing. He kills the judge instead, an innocent bystander with far too much power. Will Graham will be declared innocent. He will.
Hannibal insists that he does this all because Will is too interesting to be merely done away with. But, sometimes, all of the words Bedelia has ever said about his relationship with Will Graham float through his mind, and he realizes, when his gaze drifts to Will Graham's hair of its own accord, that he wants to run his fingers through the curls and tug on them. When his eyes linger on Will Graham's lips for just a little too long, he realizes that he wants to kiss them. Hannibal realizes that he has feelings for Will Graham that he has never felt for anyone before.
And a small, teeny part of him whispers, Is that why you find him so interesting?