Some bits of deleted script may point to taking Will's character in a different direction than they actually ended up with... I get the feeling that some got shaved off for time, but then other parts were cut in order to help change what could've been the original direction for his character.
And so there's occasionally this weird ambiguity of interpretation where some lines that made it seem to still serve that original direction but the expansion on those lines was cut out. You only get a small chunk of what was initially written, the rest is left as potential implication: it's up to you to predict whether Will's character arc is heading toward an acceptance of his true self - and being with Hannibal in some capacity - or if he got tragically "stuck" on Hannibal and the obsession born from his neuro/psychopathology will kill them both eventually. The second view would be the more practical one. And you can actually read it either way - until they left the ambiguity behind in the writer's room.
Some people may have thought they were just watching the terrible downfall of a relatively good man who was rendered prone to instability and influence by the natural qualities of his mind; in a sense, they were. They missed the details and character quirks that indicated otherwise. But then the third season got serious about the characters officially being two sides of the same coin all along - they do complete each other, and Will is a morally gray, skilled manipulator who spent his life denying his nature to his own detriment. His arc reveals itself to be a story about the road to self-actualization and self-acceptance, breaking norms and expectations. Doing things because you want to, not because you believe you're unflinchingly obligated to. Finding your own kind of love with someone you're explicitly not supposed to love - someone you don't want to love because you know you shouldn't.
So..... .. .. . I see how they lost viewers at the end there.
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