One common element is the crossover of characters. Naruto characters might find themselves in the Sailor Moon world or vice versa. Another is the combination of powers. For example, Naruto's Rasengan combined with Sailor Moon's Moon Healing Escalation. Also, the themes of friendship and fighting for what's right are often emphasized, just like in the original series.
Common elements include the exploration of how different powers work together. Maybe Sailor Mars' fire powers and Sasuke's fire - based jutsu could be compared or combined. The idea of a shared threat is also popular. This could be an evil force that neither the Naruto universe nor the Sailor Moon universe could defeat alone. Additionally, the fanfics often play with the concept of how the different cultures in the two universes would interact, such as the ninja culture and the magical girl culture.