KnK is really lacking because the source material is probably garbage (haven't read it, but that's what I'm assuming).
The directing was "generally" fine - the setting (backgrounds, locals etc.) is nice, the storyboarding and editing were generally well done (some cuts in the action scene from the beginning of episode two were edited in a weird way though) and you can't really say the animation is lacking in any way.
The biggest directorial fault were some really weird scene transitions, especially in episode 3 (this goes hand in hand with the script though). Many jumps between characters without much reason, especially the jumps to the new hunter dude with the glasses who was there to... fuck me if the show told me any substantial reason for his presence. You don't really get what the story tries to focus on and there's no sense of build up or urgency, even though the episode required them. Some scenes have no place at all - like the scene with Akihito making his dinner. That indeed was bad directing. They should have left it out, because it makes his entry at the end of the episode a lot more believable (you can just assume he kept following Mirai in secret). With that scene left in, it's rather hard to buy that Akihito had time to go home, fret around a bit, THEN run after Mirai and somehow reach her in the nick of time etc. It's bad storyboarding and editing. If they just had to leave that scene in, they should have placed it earlier than they did.
Either way, as far as mise en scene goes Ishidate and the rest of the directors did a decent job. They didn't do the best they could have. And I think this can be blamed back on Ishidate because he said he did not want or feel the need to change the story much. They should have changed it more. I hear there are changes from the novel, but if they are they certainly feel half assed and half implemented.