In Eternal Wings, while Kalas appears to be Easily Forgiven by his comrades after he comes back from his FaceHeel Turn since they don't mention his part in the current disaster very often. When you think about it makes sense, after all. If they mentioned it to the majority of the populace, they'd have no doubt turned into an angry mob and torn him apart.
The audio of for the voices in the first Baten Kaitos game is recorded strangely, so it sounds like the actors are speaking through cardboard tubes. This is supposed to emulate the player (who is an actual character) listening on on their conversations from another dimension. In the prequel, Baten Kaitos Origins, the voices are recorded normally. I always thought this was simply out of backlash for the cardboard tube recording from the original, which it probably was, but then I realized something. While the player is once again an actual character who guides the main character, the player's character isn't a guardian spirit from another dimension, but instead is literally a part of the main character. In Origins, the player isn't listening on on conversations; you exist inside the hero and are in the same dimension as everyone else, so it would make sense that you're not hearing things through the filter this time around. I don't know if that was intended or not. If it wasn't, it's a cool side effect. If it was, though... brilliance.
When you visit Moonguile Forest in Origins, Sagi remarks that "there's something about this place." It seems odd for him to comment on that place specifically. But remember, the End Magnus sealed there is "Ar." That's the one that corresponds to Marno. With that in mind, it makes sense that his being there would have some kind of effect.
One of the changes to the battle system in Origins is that, instead of getting spirit attacks like in the first game, a higher bond makes you more likely to draw something you need. Given the battle system's complete overhaul, it's something you probably won't read too deeply into. As it turns out, the player avatar in Origins is not a guardian spirit. The one true spiriter in the game, Baelheit, uses some of the spirit attacks from the first game in his battle with you.
In Eternal Wings, we see that Savyna is guilt-ridden over killing a little Azhani girl's father right in front of her, which she later tries to make up for. Considering all the other things that she did during that time, it's sort of surprising that this particular memory would haunt her... but then, in Origins, we see the little girl Savyna witnesses her father's death at the hands of Sagi.
Fridge Horror / Fridge Brilliance: If there were such a thing as a Fridge Tearjerker, this would be it. The quest in the Nekkar Quietlands reveals that Milly used to gather stones shaped like people and line them up. She also lived a very sheltered life, and when the Magne-Roches smashes the stones, Milly becomes incredibly upset. Those stones were probably the closest things Milly had to friends growing up!
Combining two plot twists from the two games: You find out in BK that Melodia came back wrong having a piece of Malpercio in her. You find out in BKO that Sagi has a piece of Malpercio in him. Sagi is sort of an anti-spiriter called a maldeiter because of this. By extension you can say that Melodia was also a maldeiter.