I think your opinions here are very valid. Regarding your first point about Daisy, I think they would have stayed the same because the guardian IS the second draft. Daisy staying the same would mean that they decides they got her pretty much right from the start. "Daisy" isn't the concept they were developing, the concept was a dream person connected to the tadpole and facilitating interactions with the tadpole and the powers it gave you. The Guardian was their next attempt to improve that after Daisy.

As for everything else you've said, I agree fully. Though even back in EA I honestly never imagined we would find a way to actually remove the tadpoles before the end of the game. Maybe before the last mission at EARLIEST. There's no way of knowing that, but that's just my take. I just never expected much from the writing of this game, but that's an aside.