There was lack of characterization in FF6. Something things about their past did not make sense. Seltzer had absolutely no history what so ever. The characters had only a very brief synopsis about their history; one defining moment about them. That's it. No motivation, no aspirations, no why's or what's. The story was extremely good. But the characters were shallow. The huge cast made it worst.
The religion controversy in FF10 was well done. The people of Spira were ingrained with a false sense of purpose and servitude towards Yevon. Some might call this an atheistic agenda others may call it a example of religous propaganda. It touched on touchy issues. The characters were not all the same. They had different beliefs and different perspectives on Yevon. Wakka was extremely devout. Lulu was devout but pensieve. Rikku was against Yevon. And Kimahri and Auron just plain didn't give a sh** about the matter. The characters were diverse and had deep psychological/moral issues embedded within them. They had many layers of personalities.
The enemy wasn't really Sin. The enemy was their own religion. Their entire religious upbringing was a total lie and farce. Imagine if Christianity was proven to be a lie. Millions of people would be devastated. Sin was just a metaphor for corruption. Power, prestige and greed were the sources for corruption.
All in all the story was WAY deeper than FF6. An educated person would have field day analyzing the FF10's story.