What irked you about Naoto?
The romantic arc specifically. The fact that the game rewards you for pressuring her into a particular gender role was agitating to me. Possible cultural or fanservice issues aside, it just seems incredibly dickish to try and influence something so central to a person's identity. I'm not very well versed in gender theory and don't remember the exact details so I'm not equipped to pick at it further, but it bugged me.