@ WhiteLion: First, to answer your question. To me, a good plot is either philosophical, or it has 'good execution'. I like thinking (a fact demonstrated by my love of Eva) and so I naturally lean towards the Xenogears-type games. It might also be that JRPGs heavy in philosophy tend to lack pre-adult characters, emphasizing the maturity level. I can't really describe what 'good execution' is. I suppose it's when a tried-and-true formula is used and it's somehow better than all the cliche-ridden crap. An example of this for me would be Atelier Iris 2. Aside from getting rid of random encounters and actually adding strategy into the battle system, I can't really think of how a 'good' RPG would be made.
I definitely tend towards mature and serious material. Philosophizing has its ups and downs. Trigun and Death Note were great anime series because of their philosophical aspects. They both presented moralities in which characters weren't merely fighting for some vague notion of good and truth, and the morality was not black and white, but rather blurred together and raised serious questions for the viewer. NGE, to me, goes the way of Xenosaga, having some potential and interesting ideas, but eventually drowning itself in a convoluted web of ambiguous and at times misapplied symbolism paired with heavy handed philosophizing that quickly devolves into drivel.
Good execution games also exist, and most of the RPGs I played and liked fall into this catagory: Grandia, Skies, certain FFs, etc. These games are worthwhile to play, and not by any means failures, but don't awe with their storylines.
Now for everything else: Did you at least play through Xenosaga Episode 3? I also want to say that several all of your comments about it I'd love to argue with you about, but maybe another time. Considering that you said, in another post, how you didn't like GitS and it's philosophical basis, it's not surprising. I don't think you'll like Xenogears either in that case.
I only played through Episode 1, and was tired of the game after that. Maybe Episode 3 is epic and amazing, but extreme improvement would be needed.
As for Ghost(the first movie), I think it asks a lot of pertinent questions, and the world it takes place in is an insightful and thought provoking place, but it fails on an important level: it asks important questions, but to me, it utterly fails at drawing you in and making you care about the answers. It's too close to reading a philosophy treatise: fine for thought, but not for storytelling.
Maybe my difference with you would be best summed up thusly: intelligence is important, but it is only half of what I care about. I also want a sense of passion and intimacy from plots, I want to be drawn to care about the characters and their struggles, truly be able to dislike the villains, not just be challenged to think, but to be immersed in the world and made to care about it.
I would push for you to play Odin Sphere, but considering how you are judging all aspects of it, I better not. You'll also be likely to be disappointed by Chrono Trigger. Maybe you'll even be disappointed with Shin Megami Tensei games.
Don't know until I've played them.
What are you looking for anyway? Grandia had a nice battle system, but the plot was simply above-average at best. So I don't think Grandia nor FF7 deserve to be affiliated with "an unprecedented level of depth".
These games innovated in gameplay and worldbuilding, not plot.
It just sounds to me that you have your expectations way too high.
That's the point of this topic. I'm not saying the games we're discussing are failures, many of them are quite good. I'm wishing for someone to create a modern masterpiece of the RPG genre, story wise, and observing that more daring innovations will be necessary to reach that level.