So I haven't figured it all out yet because it's SO SMALL... but it looks like A Link Between Worlds is using the Skyward Sword Hylian alphabet. The catch? Since Nintendo never released HOW it works or even the full alphabet (except that they themselves did show in game how to use characters with duplicate meanings, but that's beside the point)... it looks like they swapped character meanings around and added some new characters to the mix.
Yep.. it looks almost the same but the meanings of characters are different, so in essence it's a new alphabet! I'll post more on it and my findings when I can figure a little bit more out, maybe try and get some pictures for you guys. :3
Update (Dec. 3 2013 @ 6:00pm MST):
SO...it looks like Nintendo saved me the trouble on this one. There's actually an official key for this version. Kind of disappointing, I wanted to study the signs! *laughs*
for pointing it out! :3zeldawiki.org/Hylian_Language#…
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Update (Dec. 12 2013 @ 9:45pm MST):
*flails* I just cried SO HARD. Omg! I beat the game..it's so beautiful! Any of you who haven't played it yet are going to LOVE it. If Zelda games make you emotional, keep a box of tissue handy for the end. You're going to need it.
As for the Hylian in Lorule? It's upside down and backwards/mirrored (which makes sense actually). Some of them might even be sideways. I think the sign in Lorule's village says "thieves" but I can't quite tell. That's what it looked like it said when I turned my 3DS upside down, at any rate. lol