>>58008853 (OP)Well to start, N is the main rival character with a tragic backstory that's being manipulated by the main villain. He also has a design that looks cooler than your MCs', has the main region's shillmon (Zoroark) as his "ace" pokemon and he drives the plot. I see him get compared to Nagito from Danganronpa pretty often in the past, another character that girls were obsessed with. While I don't know that character and their similarities, I can assume he's another mysterious, anti-hero, pretty boy character that's important to the plot.
Overall, what makes N popular is that his character breaks the mold of rival(and even villain) characters, so much so that many people didn't consider him to be one until MasterEX.
N is the proxy leader of a team organization and is pretty antagonistic, but he never disrespects you or hates you for getting in the way. In fact, he shows admiration for you, considering you to be his true equal and someone who understands pokemon like he does. He's also honorable, letting you obtain the legendary after he did to fight him on equal footing, even healing you before the encounter. He's also the second rival to reach champion status, behind Blue. Despite this, he doesn't do it for the same reasons you or most trainers do, and him becoming the champion poses a threat to the unity of people and pokemon in Unova. And as a rival, he doesn't stick to the same team throughout the game, only using pokemon that can be found in the nearby area until the final encounter. He's also the first rival to own one of the main legendary of the region. All of that, combined with his backstory and his interactions with you in the story simply won many people over him during their playthroughs.
Tldr: N is just unique, important and sympathetic enough along with a good design to be popular.