Agreed on the comments already made upon your work. I like reading a lengthy entry. Proof of that can be seen in the winner of the first RPGC. As was said, you had a problem with making your story flow. Before I get into the meat of this, I will take a look at technical issues that might help.
I will keep getting on top of you about ellipses. I've had to do it to myself. I've loved them before but oftentimes upon a second look at my work I used them incorrectly or they were just not necessary. Hey, you can use them or not use them. That's up to you. The more important technical note is the large block paragraphs. Breaking it up more carefully based on specific details might help. The sentence structure in itself might have explained why this dragged on. AND it should not have dragged on considering the fascinating and fun story that had a lot of cool action inside of it.
And off of the technical issues, we'll see why it dragged. At least, in my opinion why it struggled to get going and gather steam. The biggest issue was exposition. You spent a lot of time and a lot of words TELLING me who these characters were and why they were doing what they were doing. I wanted to see it. I didn't feel a connection to the students that were trained by the main character. I didn't feel her passion except the exposition of her thoughts and events I never got to see/feel/hear, etc. You seemed distracted by the backstory. Perhaps the backstory was too grand for this entry, or you could have had some action sequences with dialogue where I could get a grasp of her relationship with these students and the captured girl who she switched bodies with. And I think you can make that connection with some short scenes that connect us on a human level with Eima.
I'm going to use this quote here:
A sense of extreme urgency filled Ayuna, where she was standing staring at her original body. She had to stop that man from striking her friend. She had to do it now...!
What if you wrote that as this: "Ayuna stood silent as the man abused her friend. Hatred bubbling (note: or bubbled) up in her eyes as her fingers clenched around her gun. This had to end, now."
Not perfect, but that's an example. From there the urgency is inherent from her reaction. The whole scene felt very passive in sentence structure, and a lot of telling happened. She was supposed to feel urgency, but this is ineffective if I did not feel the same urgency from that sequence. Watch out for the passive voice. Also watch out for using too many -ING's (starING, strikING) within your sentences. I'm not saying you can't use them. They're necessary but are better when they compliment the pacing of your sentences. From my view, too many "-ED" endings can feel choppy. And too many "-ING" endings can do the same thing.
You could have established things earlier within the writing as to who you were referring to. The clearing up of confusion within the story was out of place and took me out of the story. Either make a note of that in the beginning or use your writing skills to establish that within the entry.
That's what I've got for you. I think you have something really friggin' awesome here if you work on structure, phrasing, and the problems of exposition. Exposition is part of writing, and has its uses but should be placed in where it fits rather than taking over the story. Action and character should take over the story rather than the telling of it. But most of us already know that so I'll stop hammering that point into the ground. You have a super anime style of story here in its feel, AND I LOVE THAT. The powers were awesome. People jumping hundreds of feet into the air is a lot of fun. The threads of fate power was a nice twist and a power that I dug completely. Awesomeness, really.
Tons of potential here. Just gotta tap it by putting in the work, and judging by the length I don't think you'll have a problem with the work.