Suikoden 3 - Most rpg plots tell the story through one groups eyes. Suikoden 3 tells the story through four: the Zexans who live to the west, the Grasslanders who are war with the Zexans to the East, the neutral party who's journey somehow gets intertwined with the two other groups, and a final party - the villain. You can choose between three characters, the fourth is unlocked after you get all characters and beat the game. Each character has 3 chapters which serve as a prologue before the 4th chapter, when the story truly begins. This allows to show the conflict from a completely different perspective. Early in the game, Chris, the main character of the Zexen side ends up killing the best friend of the Hugo (main character of the Grasslander side). The Zexens raided a Grasslander town where the a portion of the main characters are and burned the town to the ground.
When you play as Hugo during this section of the game, it's easy to sympathize for his friend. They killed their people, burned their village down, and were causing frenzy after signing a supposed truce. So his friend was angry and tried to swipe down Chris, and failing.
Whereas, on Chris' side of the conflict you are shown a child mad rushing her with no parly. He just wants blood lust, so she defends herself.
The player is given reason to sympathize for both sides, and the story does this pretty damn well for the most part, and keeps things more human and less black and white/good and evil. That said this type of story-telling can also be seen as a curse, as it forces you to revisit certain areas multiple times with different characters to see different outcomes to the same situation, but the game does this well enough on its own to the point where it's not annoying.
It's one of the few rpgs or games period that I have played that actually took one central conflict and gave it different viewpoints. It gave each character their own role in the story, and showed the war has no good or evil. It's just people fighting for what they believe in.