I am in the boat that Uncharted 3's Elena looks a little off. It's mostly cuz of her eyes. But here's a nice video of Nolan and Emily talking about the relationship. NO SPOILERS
Starting at 50 seconds you'll see footage of what Elena originally looked like, but Naughty Dog later changed her eyes. Keep in mind the scene looks a little different in terms of lighting and details as this was an earlier build. Still, I feel that this Elena looks better than the one we got, her eyes are just too dark in both versions. She has brown, not black eyes.
Either way this is a cool video with the amazing Nolan and wonderful Emily! Enjoy!
I see a lot more Emily in Elena now than I did before in the other games. I think both her and Chloe look better in this game.