9S' descent into madness and general bad things was well done, but given the first part is mostly about 2B, you're like, ok dude, that's cool. And his madness and hate and I-ve-lost-everyone-I-ever-loved could very well have been done with 2B, given it happens just after the bunker is destroyed.
So yeah, with the dilution, I feel like what should have been strong moments have been changed into "meh, ok, I guess". Like 21O. I mean, I was crying tears of blood with "Thanks for the flowers" but with her, I was so nonplussed that I killed her before she could launch a single attack (maybe it was the fact that at this point so much shit had gone on that it was hard to have more).
Also, maybe 2A and 2B would have made for a better last fight, like Dante and Vergil in DmC3, since they're basically reflection of the same character on different levels of fucked-up-ness. Also, given the last arc is a descent for everyone but 2A, it would have made an interesting switching of place, since 2A basically is insane murder rage 2B.
So yeah, either make us care more about Nines in the first parts or replace him. Well, given this thread, apparently some people cared about him a lot at this point, granted.
Ah, also, last point, but the fact that you play 2B in the bunker makes it that her death doesn't look like the culmination of Yoko's wild ride (tm) but just another bad thing on the side (even more given the fact that gameplay wise, you're given a character that plays mostly the same so you don't really feel a sense of loss as a player).