So, I've got a theory about what Delta Rune is really about. (Credit to lots of people online whose stuff I've read that helped me crystallize this, and whose theory this probably originally is.) Delta Rune is about how a player possesses a character, and how that takes away their free will.

One immediate thing - you CAN'T actually kill anyone. No matter what happens, you get zero EXP. The choice to kill or not is a false one. But what is there under the surface is us taking over the character. The first time you save, you overwrite a save with Kris's name with your name. Lots of NPCs in the town comment on how you're behaving quite out of character for Kris (because you're not Kris, you've just taken him over.)

People have pointed out that most of the time in cutscenes, Kris just stands there - you're possessing him and not doing anything, so he's frozen. When Suzy grabs him and when he falls into the dark world, he's a rag doll. But sometimes... he acts. It's rare, but it does happen. And at the very end, in the last cutscene, when Kris literally rips out his soul and puts it in a cage... you can control the soul, and lose control of Kris.

This goes well with the stated theme of Delta Rune - "your choices don't matter". That phrase gets shoved at you a few times, and it's clearly important, but it wasn't at first obvious to me how that would make for a compelling theme. What, is the game just going to be transparently railroading you like every other game? That doesn't seem very interesting, you can't make a game have a theme just by making it linear and lampshading that.

But I think that's going to make sense because "YOUR CHOICES DON'T MATTER" is a message for KRIS. His choices don't matter because a Player is taking him over.

And THAT'S going to be the secret conflict of the rest of Delta Rune. As you play through, you'll find opportunities to see what Kris wants, for his personality to assert itself.

That's going to be the dilemma presented to the player - do you force Kris to do what you want, or do you find a way to help him get un-possessed. The "best" ending will be the one where throughout the game, you play AS Kris would. The "bad" ending is going to be the one where you stomp on his personality deliberately, to the point of throwing away his stuff. And maybe the neutral play through is going to be somewhere in the middle, where you eventually free him.