Hey the first game I nominated to make it (Xenoblade) and the first game I nominated to not make it (Radiant Historia).
Xenoblade Chronicles was the best JRPG of this generation. That's not saying a whole lot, but even in a more prosperous era it would have held it's own. I loved the characters, battles and story. The story in particular took some really interesting twists that I didn't see coming. The abilities of the characters were pretty diverse and made for several unique party set-ups. I'm getting the urge to fire this up now and try to beat some super bosses.
For those of you that like RPGs and didn't play it, give Radiant Historia for DS a try. It plays like a SNES RPG made for this era and it's really fun. There is a time travel aspect to it, but it's done really well and not disjointed like some other RPGs mentioned in that list above... The battles have a unique grid system that allows you to stack enemies and hit them all at once with the right abilities. I had a lot of fun with it.
