I think one of the key mistakes is thinking "On the run" means "procedural". It just means you have Hannibal Lecter out loose in the world which basically opens up the storytelling to go anywhere.

"Season three is going to be a lot of fun because it’s going to be taking a lot of disparate elements from the novel ‘Hannibal Rising’ and the novel ‘Hannibal’ and mashing them up together as part of the thrust of the season. It’s going to be fun to bastardize two novels into one sort of Frankenstein season."

"My hope is that not only do we have a completely different Hannibal Lecter story in season three, but we will meet some of those great characters like Francis Dolarhyde and Lady Murasaki and weave them into the world in a unique way."

Having Hannibal on the loose opens up a world of options. Even if Will is chasing him, he is just another vehicle to take us through Hannibal's backstory.