Might get some flack for this, but I genuinely think the 'most popular' list gets skewed by what's been updating recently. The real enduring hits for Ruby x Aqua? Honestly, you gotta look past the big numbers on Archive of Our Own sometimes. There's this one called 'Respawn' that kinda got me hooked—it's an AU where instead of the showbiz plot, they're stuck in a death game loop together. The dynamic shifts completely; all that intense co-dependency from the series gets warped into something even more desperate. It's not the most kudos'd thing ever, but the comments section is a whole cult following.
Lately I've seen a ton of 'Idol Producer' AUs blowing up, which is... fitting, I guess? But they can feel a bit samey. The standouts are the ones that dig into the reincarnation angst everyone tiptoes around in the main story. 'Double Blind' handles it best—explores the horror of maybe recognizing someone's soul before you remember your own past. Makes the romance hit way different, almost tragic. That one's definitely in the top five for the pairing, at least in terms of discussion threads I follow.
End of the day, I'd sort by bookmarks instead of kudos if you want quality. The popular fast-food fluff is fun, but the stories people actually save and re-read tend to be the heavier character studies.