Actually, It was pretty good pulled off in Fallout 3, you had like dozens of different endings and dozens of different paths, which eventually, of course ended up in 1 story line with different outcomes.
But in Aquaria you only once have a choice of path... and further it's only exploring, so I have to give you that. None the less, that doesn't matter to me, the creators of the game are responsible for creating the story, and a damn good one, which Bit-blot has certainly done.
Not a while ago I found a rather interesting piece of dialog that was not used in the story, I'll post it here.
"Creature: Who goes there?"
"Naija: It... it is I, Naija."
"Creature: Naija... what a beautiful name."
"Naija: Beautiful?"
"Creature: Come closer, little Naija."
"Naija: ..."
"Naija: In the name of the Old Father! What kind of foul creature are you?"
"Nerhaji: Ha! Foul? I am Nerhaji! Once I was as mighty a God as any. Now reduced to this form... it is more than foul, it is sacrilege."
"Naija: What? Put me down!"
"Nerhaji: You are a defiant one, indeed. One I would have called a sinner, so long ago. One who would have been fed to me, as nothing more than a tasty morsel."
"Naija: *pain* Let... me... go!"
"Nerhaji: This pain you feel Naija, does it make you feel alive?"
"Naija: *pain* What...?"
"Nerhaji: Your bones could be crushed in an instant. Your spirit extinguished from this realm forever."
"Naija: *pain* ..."
"Nerhaji: You may very well be asking yourself, 'Why am I still alive?'"
"Nerhaji: The answer is simple."
"Nerhaji: It is by my grace that you are allowed to continue squirming in my mighty grasp."
"Nerhaji: For you see, Naija; I need something from you."
"Nerhaji: I require a gift, and it is a gift that even a frail mortal as yourself, can provide."
"Naija: *pain* What... do you want..."
"Nerhaji: Quite simply, Naija, I am old. I am tired."
"Nerhaji: I have spent an eternity in this place, longing to be free."
"Naija: *pain* What... makes you think... that I would free you..."
"Nerhaji: Ha! As if I would desire to rule in this dying age. No, Naija... I wish to be free from existence."
"Naija: You want to... die?"
"Nerhaji: What was truly me has long since died. All that remains is to free my spirit."
"Nerhaji: I will teach you the Song that will bind me to the void, once and for all."
Source: \scripts\maps\node_energygod.lua
For some reason I'm glad this wasn't in here. I may be very prejudging, but I don't think this would've come over right.
I'm just saying... the story is good, and looking at this text, you know the team here has put a lot of blood, sweat, tears, time and trouble into this.