Both are a thing of Beauty. Not Da Vinci beauty mind you, so I'm using the term loosely.
Grandia 2 has something going for it which most RPG's neglect nowadays: Charm. It was charming. From beginning to end. Point A to B. The characters have
relationships with one another; an addition sorely lacking in FFX (think Auron & Tidus, people). It has a
serious story? Please, it's mostly lighthearted. I agree, i'ts not without it's flaws, especially in the way the church is presented (as previously mentioned). But it is still an RPG. From what we have seen of RPG's, the stories have never been
brilliant. Xenogears was my personal fave, but there are huge presentation issues, not to mention Takahashi's addition of naivete. Planescape? Presentation and characterisation; again. Whilst it has a great existential quest, it sorely lacked visual impact and failed upon that niggling little point: character relationships. A tie in? See beginning of paragraph. But realy, Grandia 2's just great fun. FUN. Man, those were the days. When games were FUN...
Skies, whilst generally more polished, had a simpler battle system and a slightly weaker soundtrack; though both of these are wonderful in their own right. I still love those boss battles where the main theme cycles through arbitrarily...good times. But the story and charachters are, well...bigger. It's
grander in every sense. Kind of ironic, if you notice the incredibly bad pun.
But regardless of what this schmuck feels, they're both brilliant games. Personally, my RPG whore is still Xenogears, but these two rank amongst my all time faves.