The Last Story has a lot of great ideas and a fantastic battle system, but it's also thrown together really poorly. The story's a total mess. There's no grinding, but it's still too easy to get poorly-balanced stats. And there's some graphical issues as well.
Whaaaaaaaat?!?! The story in The Last Story is not a mess at all -- in fact, it holds together better than just about any other JRPG storyline told in the past decade! The complaints people have about it tend to be that it's too "small" a story, focused on overly ordinary people doing overly ordinary things, but I think that's part of its charm. Its characters are believable and relatable, and its events are all given appropriate weight and backstory to fit into the game world without seeming contrived or convenient. It's one of those rare instances where you have a story told with absolutely NO plot holes and NO irrelevant details, and as a result, it's very no-nonsense, concise and extraordinarily immersive. At least, to me.
Either way, calling it "a total mess" makes no sense at all. That suggests a story rife with pacing issues and plot inconsistencies, whereas The Last Story is more like a meticulously-crafted short story with no filler.
Also, I'm going to have to strongly disagree that it's "too easy to get poorly-balanced stats," as frankly, I don't see how that's even possible. The Last Story may be a lot of things, but (save for some optional scenarios) challenging is not one of them -- it's a story to be experienced, not an obstacle to be surmounted, and it's very generous with its "extra lives." I really can't see the majority of players winding up with poorly-balanced stats at all.
Getting back on topic, Pandora's Tower is indeed a very different game from The Last Story -- it's longer, more action-packed and less story-centric. Illusion of Gaia is a fair comparison, though I think it might be more appropriate to compare it with a top-notch Castlevania game that bases much of its dungeon design around the hookshot from Zelda.
-Tom