Kaitlyn Dever as Ellie
I personally think Kaitlyn Dever is best choice for the role of Ellie in the film adaption we currently have (outside from casting an unknown).
I saw her name pop up in a fan casting a while back and wasn't convinced. So I watched Short Term 12 and I was sold in the first scene she was in. Her tone of voice, her delivery and her mannerisms are so similar to Ellie's that playing the character would be really natural for her. And isn't that we want in the film? For the characters to appear natural, not like someone is trying to get the accent right (the popular choice Maisie Williams is from the UK remember).
The physical resemblance is also a lot more striking with Kaitlyn Dever too, when she's not wearing heaps of make up you can see she was the same freckle patches under her eyes like Ellie.
http://41.media.tumblr.com/382dc675ad9ef06d3e946c91e582fcdb/tumblr_o3ge1d90by1rg4hwho1_500.jpg
http://41.media.tumblr.com/55ae9a78fd540a4f7e0279a6459c0900/tumblr_o3ge1d90by1rg4hwho2_400.png
Neil Druckmann is also following her on Twitter, I'm hoping this means he's also considering her. It'd be the better choice over Maisie Williams