Fire Emblem: Path of Radiance has superb writing and characters, and while it isn't the hardest in the series, it is in my opinion the best, and has more than enough replay value for multiple playthroughs. I discover something new every time I play it.
Baten Kaitos Origins is just amazing (not to be confused with Eternal Wings and the Lost Ocean, which I personally think is deep fried awful). Origins boasts a fast-paced innovative battle system, creative and colorful visuals, and some of the best writing I've ever seen, story wise and especially for the three main characters, who all act like real people and have their own secrets and depths without ever getting too wrapped up in themselves. It's truly a gem, and I wish more people played it.
I also adore The Legend of Zelda: The Wind Waker and Paper Mario: The Thousand Year Door, but I probably don't need to justify those as much.