One way is through the education system. The ninja academy in Naruto could start teaching about Pokemon. Young ninjas would learn about different Pokemon types and how to handle them. In the Pokemon world, trainers could learn some ninja skills like stealth and how to use shurikens. Another aspect is the clothing. Naruto could start wearing a Pokemon - inspired jacket, and Pokemon trainers could don ninja - like boots.
The two worlds' cultures can be blended by their communication methods. In the Naruto Legendary Pokemon fanfiction, ninjas could use Pokemon to send messages, like using Pidgey instead of carrier pigeons. For celebrations, there could be festivals that combine Naruto - style fireworks with Pokemon - themed parades. And when it comes to combat, ninjas could incorporate Pokemon moves into their fighting styles, and Pokemon could learn some ninja - style jutsu.