I think it's a toss-up. Deku has potential and is constantly evolving, but Naruto's strength and strategic thinking give him an edge. It could come down to the specific circumstances of the fight.
Naruto's outgoing and boisterous personality would make Deku more confident. He would probably be more upfront and less shy. Naruto's strong sense of justice would also intensify Deku's already existing desire to help others.
In a fanfiction where Naruto is reborn as Deku, there would be a lot of potential for unique storylines. Naruto's experience with facing powerful enemies in the Naruto world could give Deku an edge. He might be more aggressive in battles compared to the original Deku. Also, Naruto's ability to make friends and form bonds could strengthen Deku's relationships with his classmates even further. And his understanding of power and how to grow stronger could lead to a faster development of Deku's abilities.
Well, perhaps the plot could revolve around a tournament. In this 'naruto luffy deku crossover fanfiction', they all enter a huge, multiverse - wide tournament. Naruto shows off his cool jutsu, Luffy surprises everyone with his stretching attacks, and Deku displays his newfound strength. Along the way, they have to team up against some really tough opponents who don't play fair, and they grow closer as friends.
In 'deku meets future deku fanfiction', perhaps the future Deku warns the present one about upcoming threats. He could tell him about villains he'll face in the future and how to defeat them. This would give the present Deku an edge in his battles and also in his growth as a hero.
Another plot might involve the older Deku being from an alternate timeline. He shows the younger Deku different ways he could have developed his skills and relationships, which makes the younger Deku reevaluate his own path as a hero.
In the manga, Deku experiences various ups and downs. He not only becomes stronger physically but also matures emotionally as he takes on greater responsibilities. There are also many unexpected plot twists that shape his journey.
It could lead to a completely different character dynamic and story arc. Maybe she'd face different challenges and have a unique perspective on being a hero.
The main differences are in their expressions and some minor details of personality. In the manga, Deku might seem a bit more intense, while in the anime, he's sometimes presented a bit softer.