A possible crossover is a power - sharing one. Naruto could share his Rasengan technique with Zelda, who then modifies it using her magic to create a new and powerful attack. This would be a cool combination of ninja and magic powers.
In a more complex crossover, the villains from both universes could team up. Ganon and Orochimaru could form an alliance. Naruto and Zelda would then have to put aside their differences and combine their forces, along with their friends and allies from both worlds, to defeat this powerful and evil union.