I've seen a lot of Itachi/Naruto fics go off the rails by making their conflicts too simple. They'll have Naruto rage about the Uchiha massacre for a chapter, then Itachi gives a sad speech and suddenly they're making out. It feels cheap. The more interesting ones I've read dig into the fact that Naruto's entire life mission is about connection and forgiveness, while Itachi's is built on atonement through isolation. That's a real clash. Naruto wouldn't just accept Itachi's reasons; he'd argue that there's always another way, because that's his core belief. The good fics let that argument breathe over many chapters, with Naruto's stubborn optimism grating against Itachi's weary fatalism.
A specific dynamic I like is when authors use the Nine-Tails as a twist. Itachi is a genjutsu master, but what happens when Kurama's chakra disrupts those illusions, forcing raw, unfiltered emotional confrontation? I read one where Naruto, in a fit of anger, forces Itachi to feel the loneliness and pain he inflicted through a genjutsu backlash. It was brutal, but it created a path to understanding that felt earned, not just like plot convenience. The relationship builds from that shared, horrific empathy.
Honestly, the worst-handled conflicts are the ones that sideline Sasuke entirely. He's the emotional pivot for both of them. Ignoring that makes the whole dynamic feel weightless. The tension should come from Naruto wrestling with loving someone who hurt his best friend so deeply, and Itachi grappling with the fact that his little brother found a person who embodies everything he failed to protect. That triangle, even if it's just emotional, is where the real meat of the conflict lies.