To be honest, I had a feeling that she suddenly was able to break the Geass on her eyes, when she suddenly knew where the Switch (or Key as she was calling it) for the Flare. That was a pretty big hint. The opening of her eyes pretty much just stole it though.
Still, seeing Nunnally with Eyes is rather something of a shocker to me. We've seen them when she was a child, but it just feels odd to see them when she's older.
Anyways, as for the episode itself? I was expecting it to be far worse, especially since I didn't think they would have enough time to work all they had into the episode, but they did. Although, I am surprised that Lelouch allowed Schneizal to live and just Geass'd him. Feels a bit forced, but whatever.