I thought the final "normal" boss being A2/9S was great, and far more impactful than just fighting another giant machine. I love how it comes right after the seamless tag-team boss battle against Ko-Shi and Ro-Shi, as that fight ends with both of them on opposite sides of each other. Then as they speak, it just slowly dawns on you that you're gonna have to choose one to play as in order to kill the other.... It was a great feeling, And regardless of what happens, 9S loses, because of course he does. Dude was crazy af.
The only thing I strongly desired from this game is more time with both A2 and Popola and Devola.
Yep I definitely agree with everything you said with the final bout, but personally I was just expecting the unexpected. You could see A2 & 9S were going to clash since he witnessed 2B's stab, when I was going into that tower I was expecting all kinds of crazy shit in terms of battles/bosses but not a lot happened.
But yeah when I got to the library the feels from the original Nier rushed through me, could have made an interesting scene to see Popola and Devola climb the tower with A2 and experience that room.