Well, the chakra system in Naruto could potentially interact with the devil fruits in One Piece. For example, a character with a devil fruit power might be able to use chakra in a new way. The Hokage, being masters of chakra, could study the devil fruits and find a way to either replicate their powers or counter them. Maybe a Sharingan user could predict the movements of a Logia type devil fruit user better.
In a fanfiction, the power-ups in both worlds could also be combined. For instance, when a character in Naruto achieves Sage Mode, they could combine it with a power from One Piece. Imagine Naruto in Sage Mode using the power of a Zoan type devil fruit. The Hokage could also develop new jutsu based on the unique powers they observe in the One Piece world, like creating a jutsu inspired by Luffy's Gear Second.
The power systems could also clash in interesting ways. The Haki in One Piece, which is a form of spiritual energy, could have an unexpected reaction when in contact with chakra. It could either disrupt chakra flow or enhance it. And the different levels of power in both worlds, like the Kage levels in Naruto and the Yonko levels in One Piece, could lead to some intense battles and power struggles in the fanfiction.