Ok, i've got a lot of time on my hands so here's my suggestion
story:
There's god, the devil, angels, demons and the soul assemblers or whatever. Soul assemblers where mortals destined for hell and given this role as thier last means of redemption, if they saved enough souls they'd be admitted into heaven and vice versa. The more stages you complete the further up the stairway to heaven you go (like u suggested).
gameplay:
basically the way it is now, since the devil wants more souls (including yours) he's gonna try to make it harder for you as you progress through the game. you could have a range of different types of souls from the innoscent (blue, slow moving) to the guilty (red, fast moving). You could have more complex terrains that involve jumping and dodging obstacles and holes in the ground, your final stage could even be in hell (like in diablo 2) complete with lava etc. Hey, you could even have demon minions running around with you trying to get the souls for themselves
would be cool if you added some greek mythology so you could have those three witches with the thread of life, so everytime they cut a thread of life, a soul appears through that portal thingy (like in disney's hercules) would really help the visuals since you'd have loads of stuff to draw.
to live is to suffer, to survive, well, thats to find meaning in the sufferening.....
