Part of The BitBeacon's impressions from PAX 2011

Regarding the 3D, I felt that it didn't do anything special for the game. It’s just kind of there. The Square Enix rep even commented on it saying they did not want to do anything gimmicky with it. At most it gives you the impression of peering inside your 3DS screen; while the UI (user interface) is present on the screen as if framing it like a picture. So it is there if you want it, but you don’t really need.

Source: BitBeacon