I agree when it comes to Pepper. I really liked them as a couple in the first two, it still worked there. But once she had a problem with something that is such a big part of Tony and that he clearly won't just give up, it fell apart there. You can't build a relationship when you need your partner to change an essential part of him/her, and that's what she is asking here. I would have preferred it if they were left as close friends or, and that would be even better, if they hadn't given her this hesitance and instead made her Rescue.
I can't see the woman who went along with SHIELD agents and helped Tony stop Obadiah (in many ways) in the first movie or that stayed and helped taking down Hammer and coordinating the evacuation as someone hating Iron Man. Maybe she's scared (for Tony and of the Iron Man, in a sense), but I still don't feel that is doing the character justice. She is kickass in her own way and it feels, to me, that they're taking it away from her by making her the nagging wife trope.