The plot matters a great deal. It could be an action - packed adventure where they save the world together, or a more slow - burn, emotional story about them falling in love while dealing with Tony's personal demons. A unique plot, like the reader being from a different dimension and Tony having to figure out how to get them back home while falling in love, would make the fic stand out.
The writing style also plays a role. A vivid and detailed writing style can really bring the story to life. If the author can describe Tony's workshop or the chemistry between the two characters in a way that makes you feel like you're there, it makes for a great fanfic. Also, how the author handles the relationship development, whether it's a quick - burn or a long - drawn - out courtship, can make it distinct.