I'm sorry to say, but I can't go any further. I've left a ton of comments, but my browser is freezing with every new comment I leave. I've spent hours plodding through and commenting already, and my normally slow review speed is just going to get slower as I have to wait for the page to reload with each comment. However, I do think I know where most of your problems lie.
But first, I want to address your synopsis.
>Parody of the 1979 science-fiction horror film "Alien". Follows the plot and setting of the film, but the protagonists of FiM (and Derpy), along with their associated characterizations, replace the film's cast.
Okay, so what are you telling the readers here? Simple. You're saying "I took Alien and replaced it with ponies." That isn't interesting. There is no explanation for why these ponies are in this situation and hold the ranks they do. Just from this, it sounds like a search and replace crossover, and those are boring as shit. Why? Because if it is literally Alien-with-ponies, why don't I spend the time I'd spend reading your story watching Alien and/or MLP? It would be a much more interesting experience. You're asking the reader to ignore everything about the MLP universe except the base characterizations and just accept that they're in this new situation that doesn't mesh with the show at all. That doesn't fly. You have to give reasons, motivations, explanations for this stuff.
Now, onto the systematic issues.
grammar was clean and shiny.
You have a detailed grasp of the setting in your mind
Your writing lacks conciseness and is wordy
Massive Show and Tell issues
Narration is often choppy and lacks flow
Phrasing and syntax issues are everywhere
Pacing is as slow as a glacier at the start
Hook seems to be missing
Let's take them one at a time.
>lacks conciseness and is wordy
In writing fiction, you don't want to take the long way around to say something. You want to say it concisely and get it out there. Otherwise, you end up with long, sprawling sentences that the reader has to pick through, digging for a small piece of not very important information.This is tiring, and quickly loses the reader's interest. If Rarity gets out of bed, say so. Maybe she does it, and wavers a little. Some description is fine, but to spend a ton of words describing something is really quite wasteful and makes it hard to read for very long.
>Show and Tell
I won't tell you too much on this. Check the Editor's Omnimbus and Ezn's Guide (links in the sticky) for detailed explanation. Basically, it is a relationship between the action and the actor as defined by your sentence structure. The actor is part of the action, but isn't the active doer. Actors are doers, they should be doing the actions.
Your sentences don't flow together. The paragraphs are disjointed. Really, there is no linkage of ideas between each individual part of the piece. Words relate to each other, but sentences have some relation, but more often than not it was a jagged switch of ideas. That can be a good rhetorical technique, but in this case it wasn't even close. It was often and consistent and it detracted from the story.
>Phrasing and syntax
This is... one of the more common issues that bugs me. It's hard to describe, but simply put: the way you phrase the actions is awkwardly read, and needs refining. There is no simple fix to this, I'm afraid. I will offer you the advice I've offered before: read. Read everything you can. George R.R. Martin, Anne McCaffery, Ray Bradbury, Vonnegut, etc. Anything published will have decent phrasing. Study how they phrase things and learn from it. Note: fixing your phrasing should help some of the flow and wordyness issues. The problem with your syntax is that it often implies a certain order of events that is impossible, or it will be so confusing and muddled with extraneous phrases that it is hard to discern what the main idea of the sentence is. Despite what classical literature's example teaches: the idea is not to confuse the reader.
>Pacing is slow
The first page and an eight is spend describing the machines coming on and the ponies waking up. The pacing is glacial. It takes forever for just about anything to get done in the first part of the story. It is primarily because of how much you describe. You have what seems to be a near perfect mental image of what happens, and you try and share it. Every little bit of it. You have to ease up and let some things go implied by actions and reactions. You can't describe everything.
Honestly, your hook right now is "Alien". Which is a pitiful excuse for a hook. You can't expect the idea of "oh! An Alien crossover!" is going to draw in readers very well. You need something to happen, whether it advances the Alien plot or if it is just a conflict among the characters. You need some source of conflict earlier. The closest example to this I can think of is the original Dead Space. It opens as they come out of hyper space, and in the first few minutes we get two major pieces of information: 1) the emotional hook of Issac's dead-notdead girlfriend and 2) the plot that they are there to repair a ship, which they find. It has two ways to grab you, and it works because it doesn't make you sit around waiting to be hooked, which is what I felt with your story.
This is a story obscured by many issues, but somewhere... somewhere deep, deep down there is a good idea in there waiting to be brought out well.