The Last Story - Dont have a Wii, but otherwise looks worthwhile.
Resonance of Fate - PASS, its very boring.
Star Ocean: The Last Hope (Is there a difference between PS3 and 360 versions?) - PS3 version has more content like anime drawings for the characters and more playable characters. I recommend you play this one. The combat is quite good. The story wont turn any heads but its overall a fun game to play. It has some pretty cool moments and places you visit, especially if you are a fan of the series. I havent bothered with the crafting.
Eternal Sonata (Difference between PS3 and 360 versions?) - PASS. It looks good and interesting but the combat gets very boring and repetitive fast. Add to that pacing problems where you are thrown from dungeon to dungeon with little story in between and it becomes a chore.
Pandora's Tower - Havent played, dont have a good opinion on it. There seems to be a timer on most mission that makes me think this could end up beeing annoying.
FF XIII-2 - PASS. Avoid like the plague. Save yourself for Lightining returns as it seems to be the only worthwhile FFXIII experience.
Hyperdimension Neptunia - PASS. Its just echi stuff, nothing you are gonna miss.
White Knight Chronicles 2 - PASS. Nothing epic here.
Blue Dragon - Hmm this one is a difficult one. It got too boring for me, but its not essentially a bad one. The story and feel are very Dragon Quest, but i ended up finding it too childish for my taste. Pacing is also not the best.
Rune Factory Frontier - No opinion, doubt its anything big you would be missing.
Rune Factory: Tides of Destiny - Same as before. Unless you are a big fan of the series, theres nothing special about these.
I recommend if you havent played yet:
Tales of Vesperia
Tales of Xillia
Valkyria Chronicles
Star Ocean 4 (already had)
Sadly thats about all thats worth it for this gen so far. Its been weak as we all know. On portables you got Tales of the Abyss (3DS) and Persona 4 golden (Vita). I dont have a Wii but i reckon Xenoblade Chronicles is quite good aswell.
I see some people recommending Lost Odyssey. It was so so to me. Definitly felt more like an FF than FFXIII, but the story really didnt turn any heads. The combat balance can be quite frustrating aswell. I played it till the 4th disc before i gave up out of boredom. Not totally bad.