Vesperia to me is like how a lot of people talk about Mass Effect 2 having good character moments, but a shit main story.
Vesperia's cast is one of the best in the series, and Yuri is one of my favorite protagonists in all of JRPGs. I found the dynamic of ideals that he has with Flynn to be one of the more interesting things in the whole game. Yuri making some controversial choices on how to handle certain villains was an amazing build up.
Unfortunately, this whole set up takes a backseat to the actual final threat that shows up near the end of the game and the pay off really putters out. So while these events do match up with the final "villain" and their motivations thematically, the more interesting way of exploring those themes through Yuri and Flynn's clash of ideals take a back seat to a typical dull and super anime exploration of the theme with the classic cliche of world ending consequences.
Having said all of that, I still love Vesperia for what it is. The definitive edition even added some laughs for me with the very poorly tacked on English dub and the awfully shoehorned in pirate girl that slows the pacing down even more.