You know, Franklyn was quite intuitive. He was able to correctly deduce that Tobias was a psychopath and that he was in fact using Franklyn as a means of communication with Hannibal. My headcanon is that Hannibal didn’t mind Franklyn except for the reason that Franklyn had no composure or dignity. Franklyn let his thoughts and impulses control him and his latent intelligence didn’t compensate for his patheticness. Then you look at Will who is also in the same grain of intelligence; he intuitively connects dots to reach a fairly accurate conclusion and Hannibal respects it because Will is incredibly self-aware and self-contained (until Hannibal messes with him, of course). There’s no reason for this, I just find it interesting how Hannibal relates to differently similar people