Naruto's chakra control could be translated into better energy management for the zanpakuto. His ability to build and control large amounts of chakra means the zanpakuto could have more powerful and sustained energy attacks. For example, the zanpakuto could have a new 'chakra - enhanced strike' ability.
Well, Naruto's movement skills, which he developed through his ninja training, could be transferred to Yoruichi's zanpakuto. Since Yoruichi is known for her speed, with Naruto's skills, the zanpakuto could gain an even greater level of agility. Maybe it could move on its own in a more acrobatic way during combat, like Naruto dodging attacks. Also, Naruto's ability to sense danger and opponents' presence could be turned into a new feature of the zanpakuto, allowing Yoruichi to better anticipate her enemies' moves.