Lrt I really like that scene, not only because of what it means for Waver but for Gilgamesh as well. We have to remember that Gilgamesh (in FZ) murders his way through this thing. Backstabs his own master. Tries to win over Saber and tries to make her submissive. But-
-just this one moment, he showed something. Something he didn't show in FZ that often. He showed respect. Kindness (in a way) and upholding honor. He felt that Iskandar was worthy so he felt that he must honor him. And when Waver said that Iskandar had told him to live-
-Gilgamesh respected that. He could have killed Waver. It wouldn't have been out of chara for him. It would actually solidify his characterization in FZ as completely villainous. But leaving Waver alive because Iskandar told Waver to live showed that-
-there was SOMETHING left in Gilgamesh. He wasn't just a one toned villain who just enjoys getting his way and being narcissistic as heck. He had more to him. And that Maybe. Just Maybe. He might actually have been a pretty decent guy (which we learn is true in FGO).