It's easy - Lecter is the villain of the story, and the FBI agent is the protagonist and the person we sympathize with. He suspects out that Lecter is a serial killer but for whatever psychologically based reason, he can't bring himself to expose his crimes.
, but with Doakes as the protagonist, and also with Doakes having more psychological attachment to Dexter and not just being out to get him so that their push-pull relationship can last for more than just two seasons.
They can get 4 or 5 cable-length seasons out of that premise. And maybe they'll figure out more complications to toss in. The FBI agent might have other plotlines that have nothing to do with Lecter.
Or, if the writers are really good, they might be able to get away with having a sociopath like Lecter as a semi-protagonist, just because he's so funny and slick and the audience will like him. Tricky, but theoretically possible. And we have the "out" of the FBI profiler if Lecter makes us feel too creepy about ourselves.