I have the notion of a sort of Morality system, something that could and SHOULD have been seen in Fates.
Shura was actually a good example of this, and is about as close as we got to my idea.
But take a enemy boss, sort of a freedom fighter, at first glance he's just a rebel but through context we can learn about him and his cause. Once beaten the player may be presented with a choice on saving or sparing him. Sparing him may allow him to appear later on as an ally, or possibly be recruited while killing him may gain rewards, or it may not.
Allowing the player some choice in the actions and morality of the protagonist leads to interesting roads for them, especially if it can be tracked properly. Why spare X but not Y later on? Did group A deserve to live while group B was punished? Varying paths with multiple results.
If done right, and it is likely a monster to properly imbed into something like a GBA rom, but XNA or SRPG studio might allow for more flexibility.