Ending E is so great in it's subtlety. It manages not to take away the gravity of the previous endings, and it doesn't pretend that hope itself is going to solve every problem the newly revived 2B, 9S, and A2 will encounter. We know 2B and 9S will have a lot of internal struggle to deal with, given this "second chance". We know A2 is still alone, we know the moon bunker and the Operators are all still gone and that the Devola and Popola models (the only healing models) are now completely wiped out as well. The earth is in shambles. It's not going to be an easy life.
Ending E is more about freedom, and the human capacity for love (vs the brutalities and cruel acts we see in the game) than giving the audience some sappy ending, which I think is really nice. Especially for 2B, who never really had the chance to redeem herself or to fight for anyone she loved. She had to kill 9S over and over. She was obviously fond of 6O, but did not want to get heavily attached to any other Yorha models, and during that fight in the forest, she likely very well knew what A2 was talking about even if she didn't have all of the details. 6O is still gone, and the Resistance, if they could even still be called that, obviously are going through difficult times. However, 2B and 9S are free. A2 is free. Resistance members are free. Everyone is able to find their own purpose, and to explore the more optimistic aspects of humanity
I caught that too. I think it's a continuity oversight, since the files from the resource collectors are being read by 9S.
It really undermined the reveal for me, honestly. I don't know why they did it but it doesn't feel intentional.
Yeah, that was strange. I felt like maybe it was a "last straw" kind of moment for him. I don't know what kind of "prize" he was expecting, but his mental stability just couldn't take what was going on in the tower. If he wasn't so focused on killing everything, I would be surpised that he didn't just choose to self destruct. If A2 hadn't shown up at the top, I think he would have.