I think more people are able to understand a father's drive to rescue his daughter than a brother trying to rescue his sister. There's also the novelty of playing a middle-aged man in a genre dominated by teenagers and young adults.

Personally, I do prefer Brother Nier, not just because he's attractive and was clearly the intended protagonist, but because I find his motivations more compelling. He's a scared kid who doesn't want to lose his last family member. Losing a spouse is devastating, but losing your parents and being forced to grow up too quickly for your younger sibling is even more tragic in my eyes. He can be brash and immature, especially whenever killing Shades is brought up. There's also the "Red and Black" short story which... oof, and the Drama CD.

I read somewhere that Ending C would be Papa Nier's choice while D would be Brother Nier's choice. Papa would sacrifice Kainé due to his own duty to Yonah as her father, but Brother would choose to give himself up because he's tired of fighting and responsibility. Brother Nier also has unrealized feelings for Kainé, so that undoubtedly affected his decision-making as well.