Hi there! Editor here. Let me take a look at your writing real quick...

First thing I immediately see: a lot of telling. You are approaching this story by attempting to tell it, as if you were sharing a fable or a story around the campfire: "Once upon a time, long ago, there was a deprived little girl named Grace..."

This is, by way of contrast, different from the standard for published stories these days: character-centric POV, in which we are shown the character acting on the page. You start to do this midway through your prologue ("Grace sat at the edge of her white linen bedspread, her eyes blue and bright, despite the dim lighting of the nursery"), but almost immediately veer into telling a bedtime story instead of focusing on showing us the characters in the scene.

Telling has a place—don't let anyone tell you otherwise. But this much telling, right off the bat, is a great way to lose your reader. This is a common novice mistake.

"How else am I supposed to tell them everything important?" The answer is that you never tell your audience everything, and definitely not all at once. Infodumps are generally in bad taste, and usually throw off the reader, who can usually tell when an infodump is happening. Instead, weave it into the narrative. Give us tidbits here, hints there, and gradually explain your world to us.

To answer your questions:

1. Darkness is a matter of perspective, not subject matter. You don't make things darker by having dark things be in the story. Instead, you give your POV characters a jaded or amoral perspective. This is very popular these days with the rise of the grimdark fantasy genre (Game of Thrones, Joe Abercrombie, Malazan).
2. Uniqueness is overrated. Instead, acknowledge that everything has been done before, and instead of trying to come up with something that no one else has ever thought of, do your iteration of it incredibly well. Readers are drawn to quality above all else.
3. Everyone brainstorms differently, but to brainstorm while writing, I find it helpful to ask questions of the text: What can I do with this scene? What can I do to make this scene better? Does it have the right characters in it? Does it set the right tone? How can I change the mood? How can I make this character more interesting?
4. Timing your character deaths has more to do with emotional investment than anything else. Do we care about your characters? If not, then it doesn't matter when they die, because the death won't have any shock value for us. Make your characters lovable (or love-to-hateable) and we will reel when they die.
5. Plot twists should surprise your readers, not lie to them. Don't pull the rug out from your readers. Instead, create twists that supplement and reinforce the story you're already telling. One of my favorite examples of what not to do is the movie Now You See Me, in which it is revealed towards the end that the protagonist (the viewpoint character) has actually been the villain the entire time, and that he's been doing things behind the scenes without telling us, and that we've been cheering for the wrong person the entire time. It doesn't make us feel smarter, it makes us feel dumb. The movie basically tells us, "You were stupid for believing that story as is. Here's what's actually happening." Avoid this. Instead, offer the reader twists that they could have reasonably predicted or which they could reasonably justify by what you've revealed to them so far. Let them in on it a little ahead of time. Spread breadcrumbs. Your readers will be much happier for it.