This is a super-interesting question! I was jawing something related over with @wellntruly recently, to wit: a huge driver of the development of their relationship was Will trying to conceive of and act as Barbie Dress Up Murder Husband in the back half of S2. The Will that really flipped Hannibal for a loop was, in large part, Will’s construct of what Hannibal might like, the successful creation of something to project on based in part but certainly not in whole on the raw personality materials available.
But Hannibal was also outright fascinated with Original Flavor Will in S1. I don’t think Hannibal really had a paradigm for that; his MO was a sort of… forcible moulding of Promising Candidates (cf Randall Tier, the Zachary Quinto guy) that presupposed that Hannibal’s psychic driving was going to take folks to their most interesting (and, not coincidentally, murderous) place.
To my eyes, Digestivo-forward Hannibal had come to the conclusion that Will was more interesting when driving his own psyche, and his more hands-off approach (which, yes, was partially necessitated by being in prison, but then there’s how he ENDED UP in prison). I wonder if part of that was that, having had some time to reflect, Hannibal was able to identify the most dazzling moments from the back-half of Season 2 as times when Will’s Murder Barbie performance slipped. The real righteous rage aimed at Clark Ingram, for instance. I’m not sure that Randall Tier’s death would have played out so differently if Will had not been mid-entrapment (with the notable exception of the visualization of beating Hannibal specifically - maybe Season 1 Will would have seen a ravenstag, or something else slithering symbolically around in the murky soup of his psyche). I will grant the aftermath would not be the same, but the kind of… amateur-hour mounting efforts in the Natural History museum cannot possibly have been the real thrill of that experience.
And then there’s the heavy losses Hannibal has sustained along the way. I couldn’t agree more that Hannibal is not a chessmaster, especially when Will Graham, Agent of Chaos, is in the picture. His “plans” consist more of keeping a lot of resources in his back pocket and deploying them impressionistically as needed in response to outside circumstances (what @wellntruly calls Fate and Hannerstance). I don’t doubt that he’s spent some time and equations thinking on how he could’ve used different tools, made slightly different moves, in ways that did not require him to abandon his longstanding identity, to spend three years in a very boring prison, to suffer the loss of Will and his attention again and again and again.
The language is kind of forced forward by the Red Dragon, and to a lesser extent Jack, but I got the sense that Hannibal had come to appreciate Will as a dispenser of specifically violence he is willing to call “righteous.” Now he’s the Lamb of God, and Hannibal doesn’t seem too put out by that. The slaughter of the Dragon is more of a change in method than a change in action or principle from taking potshots at Garrett Jacob Hobbs and Eldon Stammetts. The aesthetics have changed. Have the ethics? I think Hannibal may gras that he might’ve got a lot more milage out of pushing the definition of “righteousness” than trying to remove it from the equation altogether.
I think I may be out on a bit of a limb here, but I see less an evolution from Regular Will to Dark Will, and more motion around him. I see much more character change in Hannibal, from icy orderly planned killer to Murder Lion, Weilder of Hammer and Teeth and Maybe Impulsive Ice-Pick, from would-be puppet-master to would-be partner. The rules of the game seem also to have changed. Alana and Jack both hardened and became more willing to deploy very dark grey, murdery schemes of their own where they felt they were “justified.” Where’s the moral distance between slaughtering Mason and slaughtering Randall Tier? Between planning a murder-suicide for the Red Dragon and carrying it out? A Will with fewer costs to count might be much more susceptible to Hannibal’s persuasion to stop berating himself for the delight when everyone around him slides toward allowing and condoning extreme acts of violence for the “special cases” that pop up right like clockwork. Then again, a Will who delights might generate much less beautiful distress, and I’m not sure that’s what Hannibal really wants, in his heart of hearts.
ETA: Given the other discussions swirling around, I don’t mean any of the above to suggest that I think Will is actually righteous, or that his violence (or Jack’s or Alana’s, or god no Hannibal’s) is ~justified,~ or even justifiable. I am actually extra-interested in the show’s interrogation of the very concept of “good violence.” A lot of my love for the show, and for Will especially, is grounded in how painful even textbook Justified Use of Force is, how ugly and complicit everyone is. One of the major “pleasures” of the show, for me, was that feeling of gradually becoming a dirty - a worse person, somehow, for every judgment I made, for every ounce of sympathy I managed to muster up, for my stomach-deep desire for Those Two Crazy Kids To Make It Work when I couldn’t justify it as a Good Outcome.