Well it's definetly great to see this story again. It's like a breath of fresh air to me.
Anyway, my favorite part of the fic has to be Kentaro and Kariya. It's an interesting dynamic because Kentaro isn't simply Kariya's 'kill that' Servant. He adds an outsider perspective on the plight of Kariya and Sakura, especially since he points out Kariya ignors Shinji's own pain. And that's the thing: Kariya's goal, while noble, is in the end selfish becase deep down he WANTS Sakura and Rin to be his daughters and Aoi to love him. In the end, that's what it is. And it's great that you actually bring this up.