Oh, durr. Yeah, I thought I had explored all of Mithalas, but clearly I missed the bit with the current.
So, now I've finished! That means comment time! Yay-hay!
First, THANK YOU for a fantastic mod. What you have achieved over 18 months of stolen time while finishing your schooling boggles my mind. You are my hero. Keep that in mind while you read the rest of my comments.
DesignGood- Sacrifice is beautifully and lovingly crafted. The attention to detail is generally on par with the main game, though some bits are stronger than others. Some parts, particularly some of the parallax effects you created, made me pause and just go, "whoa".
- The scripting and customization work you did is impressive. It's a testament to the flexibility of the Aquaria engine that you were able to do what you did. The dialog trees just work, and I thought the way the speaker's avatar fades out when they're done speaking was a nice touch.
- You reshaped the world in response to events, in a way that not even the main game attempted.
Bad- Some design decisions were questionable. For example, in the corrupted cathedral, at one point you need to swim into a wormhole in order to access another area. I only discovered this by chance because I got carried away fighting the corrupted mithalan and wasn't watching where I was swimming. In general I avoid the wormholes as a matter of course - venomous worms come out of them! Had I not gotten lucky, I fear I would have been stuck there for some time.
- The speech bubble design meant that people who could talk had to stay stationary. I once accidentally bumped a Mithalan with a rock I was towing (specifically, the scout in the kelp forest), and he went flying away, leaving an orphaned speech bubble comically floating alone. I would have relied on hover glows to signal when people can be spoken to.
Writing and StoryGood- Mostly believable as a prequel to the main game.
- Ambitious in scope. To tell the tale of the fall of Mithalas, and attempt to flesh out Mia's backstory, as well as taking a shake at explaining how the sentient races fell—well, you did a decent job of it, considering all you took on.
- Old Fred. Need I say more?

Bad- Many parts felt a bit cliched. The walker was the biggest offender here. The wizened but infuriatingly vague and unhelpful sage who sends you on silly quests is a flagrant RPG trope.
- I didn't often feel like I was doing much. Most of the action happened offstage. Now, it's fine to have lots of action offstage, but the main campaign still has to both be interesting and feel important, and it did a poor job on both counts. Luckily, exploring your beautiful levels was enjoyable enough on its own that this flaw didn't bring the mod down too far.
- In that vein, the ending was a letdown. In fact, if I had to pick the thing I liked least about the mod, it would be, hands-down, the ending.
First, we have a cutscene, wherein Mia tells all, and I'm bracing for an epic final boss battle that never came. Instead, I am teleported to a surreal half-body, half-mithals-cathedral dreamworld that I would assume is Mia's residence. Kind of fun to fight your way through, but also annoying due to the complete lack of save crystals, and also not where Mia said she would send me. In any case, after fighting my way through dangerous waters to the place where Mia waits, I thought, surely, that this would be my chance to betray her as she had narrated to a sleeping Naija that I would do—surely this would be the final showdown? No, actually; nothing really happens. Mia tells me that I "sacrificed my life", but clearly I'm still floating here, alive and kicking. Nevertheless, the game ends here, with no real resolution for Elena's character at all.
Again, this is an instance of the main character being a passive observer instead of a main player. Elena just happens to show up during Mia's confrontation with Eric, just in time to watch it go down, but without an attempt to do anything about it. Afterwords, upon confronting Mia again, Elena just sits by and lets stuff happen until the game is done. Unsatisfying.
These weaknesses are, in part, a result of the tough challenge you took on. You couldn't have Elena jsut kill Mia, and it's hard to pull off a final battle in which the player has to lose. This is part of the difficulty in telling stories through games: there's a limit to what you can have passively happen to the player, and most story elements need to emerge through the players actions. I think, however, that you could have made it work; you could have had Elena win a pyrrhic victory over Mia, which weakened (but did not kill) her, while herself being mortally wounded. Or something; I don't want to pretend to write your story for you. I'm just sitting in my armchair critiquing it. 
Sad- I never did find Fred Jr.'s brain.

Lastly, the difficulty was a bit on the easy side, even for me, and I'm below average at video games.
*whew* Sorry for the epic-length post. Got a little carried away there. Remember: you are my hero!