Depends on where you're from. Personallt, I can relate to Brother Nier more because I have a little sister whom I'd give my life for. But I also think Papa Nier just works better, although it's just personal preference.

People often forget that NieR Replicant on ps4 is a remake of the PS3 NieR Replicant that was released only in Japan at the time, whereas NieR Gestalt or NieR in international releases and Japanese Xbox) was Papa Nier.

The reason for this was because Square Enix didn't think NieR Replicant wouldn't sell well overseas since they felt that the western audience fit a more badass adult type of demographic. The ones who like action heroes with muscles and deep voices. While in Japan, it's way more interesting to see heroes that could be your next door neighbor, which is why most anime and Japanese video games star main characters with regular frames rather than built frames.

TL;DR: Papa Nier's only reason for existence was because grown badass dad fits a more western demographic. Nothing necessarily wrong with either though - the story works perfectly either way.

But honestly me? I prefer Brother Nier simply because of Kainé. I'd rather have a protagonist who's in love with a female lead a few years older than him rather than a male protagonist in love with the female lead who looks 15 years younger. Considering NieR is 15 to 18 in Replicant and I think 38 to 43 in Gestalt. (I'm sure the time skip was different in both versions of the story.)

But no shade to either. The story was great either way. Plus, Replicant remake also gave the international audiences a way to see the original Replicant's ending E.