I had Pan's somewhere in my top 20, so I'm sorry you didn't like it more. I don't feel that the characters are kept at a distance or one dimensional at all, Ofelia and Mercedes are both particularly strong characters, and I even think the evil captain is a more interesting villain than you give credit for. You compare Pan's to a multitude of other fantasy movies with similiar formulas, but honestly I think painting it in such broad strokes is a disservice to how unique and well crafted of a film it is. Pretty much any movie can be broken down into a familiar-sounding summary, but what counts is how it handled the material and the emotion it brings to it, which is where Pan's succeeds for me.
I agree with Junior that the ending is much less clear than you claim. I really think it can be interpreted either way, and I've gone back and forth on which I subscribe to.
Regarding the grape, in addition to what has already been said, I think part of it is that it's riffing on a familiar fairy-tale situation. The "forbidden fruit" that our hero knows they shouldn't take, but that draws them in with an almost magical allure, leading to dire consequences.