Finding the Hay in a Stack of Needles

http://www.fimfiction.net/story/65293/finding-the-hay-in-a-stack-of-needles

I must say that I find the concept interesting that you've put out here and by no means is this a topic to go into lightly, and it is certainly one that warrants plenty of reflection and writing. The story itself is pretty well written mechanically, it may be a bit choppy a times with far too many short clauses strung together, but none of that detracts from the storytelling, and honestly that's more than can be said for the vast, vast majority of stories on this site.
That being said, the characterization of both Rarity and Applejack had me pulling my hair out throughout the entire piece. The ways that the both of them were acting through the first chapter were implausible but possible. They don't match up with how either react to difficulty or confrontation in canon. Now granted, if there was some explanation as to how they got to those points I could understand where they were coming from, but we've seen Rarity get haughty or pouty or even whiny when she wants something, but she's been dealing with Sweetie Belle destroying various parts of her workshop for years. What in Celestia's name drives her to anger against Applejack and physical violence that she never displayed to Sweetie Belle?
And with Applejack, she's been through tougher times away from her family before, what makes it seem impossible for her to go back to the farm? Where is her thought process in this? Moreover, if I'm reading this correctly this all takes place over the course of a month and a half. A month and a half where Applejack up and leaves the farm that she had spent almost all her waking days working on, goes to Rarity and somehow gets her entire self esteem demolished, nay her entire persona destroyed. It seems in-congruent with a pony so prideful as to set up a series of competitions to prove who is best pony.
At the end of it, the characters felt generic, as though they could be replaced by anyone in the abuser and abused role. There's hardly a mention of Applejack's family or Sweet Apple Acres. There's no mention of Sweetie Belle at all so far as I can see. There's very little to actually identify the two ponies as themselves, besides the few references to Rarity dress making and the scarf. I know that everyone believe firmly in the En Medias Res, but that doesn't necessarily mean start in the middle then go back and give the full exposition from the top. I think this might have been helped a lot by starting somewhere closer to the start, such as with the first drunken night for example. What this would do is let you establish the characters as you see them and develop them to where you want them to be for Applejack's big fall. What I feel here is a massive disconnect between canon and where your characters start, and because the exposition is being told through the eyes of present Applejack we never see that development, we're just asked to accept that this is the way they both are.
This, of course, is intensified by the issue of we don't really have a good time frame for when this is happening. The best we have is the "White Maned" reference saying that it is in the distant, distant future; however it could also be a trauma so that is unclear. Without a frame of reference, it's difficult to put Rarity and Applejack in a relatable frame of mind. If they are still in their 20s, then a drunken mistake turning into a relationship makes sense, but both of them simply need to be closer to the way they are in canon because they have had less time to develop from that. Additionally, important things like Applejack's family and the CMCs need to be explained because they are such an important part of both ponies' lives. If they are older in terms of the mane reference then I'm left wondering how they get to such a state as I would expect older ponies to act in a more responsible manner in every stage of this relationship and deviations from that would also need to be explained.
At the end of the day, the story is by no means bad or poorly written. However, as I think about it, you could practically replace both characters with anyone, even two humans or any sentient beings, and the story could play out the same or even better because we aren't starting with the preconceptions of the two characters and the the questions of their history. With lack of better word, that kinda makes the entire characterization a little generic.
Anyways, that's my two bits.
Your friendly TWE,
-Duskrider