Spoiler
First, some general comments! I like your writing style, it's easy to read with nice variation in sentence length and vocabulary. I like how you can tell a pony's social status by the way they speak. However, I think this is something you need to be careful about - it may be difficult to retain consistency and, at the same time, to avoid overdoing it. I'm not saying you've had issues with this in the first chapters, just reminding that it's something to pay attention to. And the narrator's voice complicates the matter even further, of course. I think here your structuring (if that's the correct word) works very well, though: I like the 1st person and present tense used in Ch. 1 and how Tornado's personality comes through in the voice of the narrator, whereas the omniscient narrator used in the following chapters is more neutral in tone.
So far, the structure of the story appears like something you often see in movies, and I think at some point, if you wanted to, it would be possible to play with the narrator voice even further by disrupting the scene and bringing in Queen Majesty's voice, as if she was actually dictating to Tornado. But it depends on what your plans for the storyline are, and the ending especially... Adding something like that to Ch. 2 or 3, i.e. tying in Majesty's current personality, might help bridge the gap between the ruthless warrior queen of Ch. 1 and the teenage princess of Ch. 2. The queen is narrating her own life story so it would be interesting to know how she reflects on her teenage self. Well, this is just an idea, and like I said I haven't gotten very far yet, so feel free to ignore the suggestion! To conclude, I could say that your combination of G1 and G4 universes works very nicely!
I realize this will be getting loooong, but here are some chapter specific comments:
Ch. 1
I really like the "plot twist" in the middle of this chapter. The reader is kind of lulled into believing this is just another happy MLP story... and then you show us the darker side of the pony world. Now, knowing what follows, I notice some illogical word choices at the beginning of the chapter, such as "our beloved monarch" in the 2nd paragraph. More generally, too - this is Tornado's point of view, and I found it sightly confusing that he first describes the queen with such sympathy, and then proceeds to mention her fearsome reputation, giving the impression that he too is, in fact, afraid of her? I'm not sure what would be the best way to fix this - maybe the two paragraphs (14 & 15, beginning "Even standing before...") could be modified a little, adding something about the way the citizens of the Dream Valley view their sovereign? I guess what I'm after is a better link between the fact that the queen is being burdened with superficial issues like the disagreement between Glory and Surprise, and her ruthless solutions to problems, shown as out of the norm in the MLP universe.
Also, there's a syntax issue in this sentence (paragr. 15): And that's the kind of reputation my queen has earned herself [punctuation missing] a reputation as a ruthless warrior-queen who uses force instead of friendship to solve her problems, but rather bullies other ponies into doing what she wants.
A couple of smaller typos or spelling errors:
Paragraph 1, l. 1: it's --> its (again paragraph 9, l. 2)
Paragr. 9, l. 3: from accidentally repeated
Paragr. 11: do as not to --> so as not to
Paragr. 14, l. 4: oner --> one
Ch. 2
Poor Majesty!
Paragr. 6, l. 4: Not sure what 'horsemaster' refers to? Their god? Capitalising the word might do the trick.
Paragr. 12, l. 1: fort dash capitalisation missing
Paragraph 18: bowed repeated
Ch. 3
(At this point I got caught up in the story so I don't really have anything to comment on except some typos I spotted along the way. :D )
Paragr. 9, l. 2: tired --> tried
Paragr. 11, l. 2: to --> too (busy)
Paragr. 15, l. 2: int --> into
Paragr. 16, l. 1: governesses' --> governess'(s)
Paragr. 20, l. 1: say --> saw
l. 2: no comma before that
l. 3: the accidentally repeated
Paragr. 22, l 1: she's --> she'd
Ch. 4
Yay, Applejack! I'm not sure about the usage of "A.J." though. Is that what she calls herself? I notice you use the nickname interchangeably with her full name and no explanation is given when it is used for the first time, so to me it seems like laziness on the writer's part, sorry. I would either use the full name Applejack throughout, or add an introductory line, something like "My friends call me A.J." or "You can call me A.J." in the scene where she asks how Majesty knows her name.
Paragr. 18: Syntax issue "...our ancestors called this the everfree, and believed to forest had a will of their own." --> and believed that the forest had a will of its own / and believed forests to have a will of their own (I'm not sure if it was this specific forest that was referred to, or all forests).
Paragr. 25, l. 2: Something missing here? "The darkness the gloom of the shadows" (and the is accidentally repeated)
Paragr. 35, l. 1: aslready --> already (I make the same typo all the time myself, lol!)
That's it, I guess - looking forward to reading more when I have some free time again! :)