That's a little literal, remember Kaguya has a giant son complex. (It's her only real established character trait) Her making a son that doesn't betray her matches v. nicely. She's the mother of chakra, a mother in general.
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Plus in FMA, Father's Homonculus are all different voices, personalities and genders.
I still think Both Kaguya and Black Zetsu are the mastermind villain however both goes different ways since Kaguya was originally the first one who planned the Infinite Tsukoymi and turn everyone into White Zetsu so that she could nurture her planet and keeps all the chakra.
Black Zetsu was literally born right before Kaguya was sealed and he was ordered to revive her. But Kaguya didn't simply told Black Zetsu "WHAT" or "HOW" to do it. She literally entrusted him in which Black Zetsu devise his own plan and this is when he sets the foundation of Shinobi history which corrupted the system by manipulating everyone FOR CENTURIES in order to bring Kaguya back for that purpose.
When Kaguya was revived, she thought it was Indra and Asura but Black Zetsu corrected her that it was Naruto and Sasuke. Which means she has no knowledge after the Sage of 6th path era or anything about Ninjutsu and she holds no responsible for that mess which her "son" caused.
So in essence I think it all comes down to who made the most accomplishment here in this series. Kaguya made an accomplishment when she had all the chakra and use her power for herself before splitting to her own sons. She also achieved casting Infinite Tsukoymi and made everyone becoming White Zetsu which both Hagoromo and Hamura failed to prevent it.
PROBLEM is that everything takes back in the past and Kaguya was never introduced within the context of the story until near the end of this series.
Black Zetsu probably achieved the most when it comes to demonizing the world which he's able to find someone powerful like Madara who was caught in his bait in which led to the creation of the Akatsuki , however most of it was done indirectly and Black Zetsu in almost every arc had little to no roles and always rely someone so powerful to do the job for him.
I understand why Black Zetsu always being a shady type to hide lurking behind the shadow to record everything which fits his character However Kishi keeps bringing out so many Central Villains that had more impact to the story. First we thought it was Orochimaru, then it was Pain then it was Kabuto then it was Tobi who was Obito and lastly Madara.
Kishi keeps brushing Zetsu to the side so we don't deemed to find him suspicious type character just because of his design and how he act.
It's further reasoning why Suspicious characters are often too predictable in most Anime so if all this was Kishimoto intention then I suppose he KINDA made a smart play but not in a good way since we always had an impression that he was a Minor and most forgetful Character until the end of the series.
Both Black Zetsu and Kaguya intertwined each other, this is how Black Zetsu shows his true color as a powerful threat being under Kaguya sleeve.
Personally I'm always a fan of Zetsu because of how suspicious he was until Pain and then being Madara will which he becomes so irrelevant that I thought it just be me being wishful thinking that he's Final Villain when he was introduced back in Part 1 but then this whole Madara shit happen out of nowhere lol.
