I love prison era Hannibal so much, he's just treating himself and freaking people out, being the little shit he is, literally a black kitty. Will Graham's black kitty of course.
On a more serious note, I was thinking it really made sense that Will eventually chose Hannibal at this point of their story.
Putting all his personal development aside (which of course does count, the entire plot is about this, after all) to focus on the part about his love for Hannibal (which again, is very tied to his marrow, anyway, but you know what I mean), Will always had this feeling at least, if not consciously knowing that Hannibal loved him. It becomes clear to him that Hannibal is in love with him, unquestionable at this point. He doesn't have much left in him to deny the truth laid bare and plain in front of him.
When they meet again after three years, Hannibal is chained and caged indeed, but he's almost stripped of his person suit, and voluntarily so, again, almost.
It gives Will the opportunity to see him and his love for him the clearest from a safe distance, and eventually decide to freely love this Hannibal back. It was healing for them both, if you ask me.