I'd say Rogue Galaxy. It has some splendid graphics, an excellent gameplay and longevity. It was a great improvement from the previous Level 5's works, and they managed to prevent the game from becoming more and tedious as you progress, particularly in the dungeons, in contrast with what used to happen in Dark Cloud and Dark Chronicle.
The main flaw, as far as I am concerned, is the game being a bit too plethoric, something that seems to distinguish Level 5 and not only them. Too many weapons for example, and 90% of them are pretty useless since you'll probably use just two or three of them.
Anyway, a fine piece of software.