One key element is how the Kyuubi's power is incorporated into the crossover. For example, if it's a Naruto - Dragon Ball crossover, will the Kyuubi's power be on par with Saiyan power? Another is the character interactions. If Naruto meets characters from another universe, how do they communicate and react to each other? Also, the plot should make sense in the context of both universes. If it's a Naruto - Harry Potter crossover, the magic and ninja techniques need to be integrated well.
Well, the first thing to look for is the uniqueness of the crossover concept. Is it just a simple mash - up or does it bring something new? For instance, in a Naruto - Attack on Titan crossover, how the Kyuubi's power can be used against the Titans is an interesting aspect. The development of Naruto's character in the new setting is also important. In a Naruto - Gundam crossover, how Naruto's ninja values might change in a mecha - filled world. And of course, the overall world - building that combines the Naruto world and the other crossover world.