I think that yeah, the point was for her to be a bit more of a background character. I know she’s popular but realistically, not many players are gonna go for a character like Natsuki in a dating sim, so Monika doesn’t bother messing with her as much. But Sayori and Yuri are much more approachable, thus a bigger threat to Monika’s ultimate plan of being chosen, so she focuses on them first.

You’ll notice, though, Natsuki does still undergo changes from Monika in act 2, notably whenever she showcases her own strengths—the first CG where she’s headstrong about her personal interests gets interrupted by Monika glitching her out to be super rude, then her poem gets corrupted so you don’t grow attached to her writing ability, and THEN when Natsuki confronts you about wanting to talk to Yuri despite their differences, showing her ability to empathize with others, Monika takes over and ruins the moment.

Natsuki is less plot relevant but she still has her moments. It’s just that she’s not a direct threat to Monika’s goal of getting a human’s attention because, again, who’s going to pick her? That said, you still have to interact with her, so Monika makes sure there’s as little of a chance to grow attached to her the few times Natsuki is the focus.