Nagato in the original developed some actual feelings towards Kyon, but she didn't know how to actually show it to him without it being too obvious (she doesn't know about proper etiquette when approaching a male she likes because that information isn't in her databank and she's not good at improvising).
Male Nagato would have similar issues. He is interested in Kyonko, initially just as an additional strange element which can change Haruki's whims but then he notices strange feelings appearing within him. He thinks his program is faulty or just blames his human body but notices he is geniunely interested in her. But his approaches are either too shy and indirect (like leaving his jacket so Kyon doesn't get a cold or giving her a book about passionate love between high school students) or too obvious ("Hey, could you show me how your female body works?").
Also, especially at the beginning of the series, as he is used mostly to be with men he doesn't notice it is rude to stay in the room while Kyonko and Itsuko are changing clothes (with Kyonko wondering if she should throw him out or just let him be as it seems he is still reading the book) or just says unappropiate things about his body "Huh? My penis just grew suddenly? Strange, isn't it?"
After getting rid of his glasses, he also becomes extremely popular between the girls, something Kyonko doesn't seem too happy about.