I can't shake how the first time the player character meets N in Accumula town is such a y/n moment. He takes notice of you immediately and thinks you're uniquely special—meanwhile you're kinda just standing there like 🧍 Your starter, which you acquired not even 20 mins before that, takes a liking to you, and that's enough to leave him completely floored.
Ofc, growing up locked away in a tower only ever being exposed to pokemon who'd been abused means his perception of trainers is skewed, but still. Other characters instantly fawning over the MC is such a wish-fulfillment trope. N recalling the first time you two met at the end of the game just adds to the effect. That moment lives in his head rent-free!
After your meet-cute, he becomes so mystified by the player that he seeks out your opinion and wants to pick your brain at several points. N often mentions "envisioning the future," and his visions start to involve you! He muses about how you might be "an ideal trainer" to a random grunt (see the memory link flashback in chargestone cave in bw2). He deviates from ghetsis's plans by encouraging you to find the corresponding light/dark stone just so you'll challenge him in a final showdown. He goes out on quite a limb by insisting upon this.
I think my favorite moment of N being completely obsessed with the player is when he waits for you outside of the Mistralton gym for no other purpose than striking up a conversation and trying to understand you better. He doesn't battle you there, he's not accompanied by any plasma goons, and this encounter does very little to further the plot (the only plot-relevant info revealed is that there are two stones). My guy is a certified yapper, but he stops to take this moment to listen and learn about you from your pokemon.
This is also the first time when he drops his confident front, expresses uncertainty about his course of action, and sympathizes with your point of view. In a strange way, you're probably the only person he feels he can admit his self-doubts to—to everyone else in his life, he's supposed to Plasma's unwaveringly resolute King.
It's only when taking the player into consideration that N's conviction falters and his "heart wavers." Standing in front of you, the consequences of his plan suddenly become very real to him, and he's vulnerable enough to reveal his qualms about separating all Pokemon from their trainers. He even says it would break his heart to see that happen to you.
When you really examine his interactions with the player, it's clear that N's kind of besotted with the MC regardless of the gender you select. I don't even think it's a case of shipper's goggles or reading too much into things. This is just a basic reading of the text, without even even getting into the romantic subtext splattered everywhere (I could legitimately write an essay about that! Gamefreak absolutely made some choices, and it extends far beyond that moment in the ferris wheel!)
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