Been hanging around the fanfiction scene long enough to see trends come and go, and honestly, I'm starting to wonder if the 'best' Akiza x Yusei stories aren't necessarily the most popular ones. There's a whole wave of fix-its that popped up right after 'Yu-Gi-Oh! 5D's' ended, trying to smooth over that weirdly rushed ending they gave us. They're well-written technically, sure, but they often miss the tension that made the ship interesting in the first place.
What I keep going back to are the older, sometimes unfinished, ones that really dig into the psychic powers angle. 'Synchro Resonance' by that one author who vanished—such a shame. It treated their connection as this messy, volatile thing, not just a neat romance. Aki's trauma and Yusei's emotional constipation were actually obstacles, not just things to be fixed with a kiss by chapter five. The 'best' for me means stories that don't sand off their rough edges.
Most of the rec lists will point you to the usual suspects on AO3 with thousands of kudos, and hey, some of them are fantastic. But don't sleep on smaller, character-study pieces on FFN or even tucked away in forum archives. They can have this raw, intense focus on just the two of them that the longer, plot-heavy fics sometimes lose.