As I understand the story, Cranky takes the lesson from Pinkie's intervention that unexpected good things have to come to him via ponies he personally dislikes, discovers to his disappointment that his character growth has made him get along with nearly everyone, is relieved to discover that the MLM pony sucks enough to hate her, and then is disappointed to discover that in fact this formula doesn't work when she tries to pass off Fluttershy as his son and Fluttershy tries to justify the whole setup with a fairly nonsensical moral. That's not literally incoherent - Cranky's actions follow from his beliefs, and his belief in a loose sense follows from his experiences - but it does require Cranky to be kind of a psychologically bizarre alien. I'm not sure if this is meant to be a sort of lolrandom comedy that just doesn't match my sense of humor, or if I'm just missing the point entirely.

>>Chris
I have to ask: what was the poopfic-off?

The tense thing didn't particularly stand out to me - the second sentence making explicit the passage of time relative to the first made the tense shift feel very natural. I agree with >>Baal Bunny that "a couple hours" seems much too long for Applejack to wait before going outside, but I don't think much changes otherwise if she only waits a couple minutes. The sentence structure at the beginning is a bit repetitive - your first six lines are all "some assertion" "But, contrary assertion" (and the sixth line even includes both halves of that pattern another time in the description of Winona's growls), and it would be nice for that to vary a bit more.
Rainbow Dash characterization was great, not just in her competition with Winona (which, to be clear, was fantastic), but also just in all the individual exchanges with Applejack.
The ending was definitely the weakest point - it felt to me like you were trying to append a moral to a story that didn't really need one.

On the whole, though, I really enjoyed this - the complaints I have are very minor details, and the substance of the story felt very strong both in concept and execution.

I think my main issue with this story is that the impact of the ending hinges on Celestia being right that she could have predicted Luna going evil, and we just don't get much reason to believe that's true (Star Swirl says it is, more or less, and by convention the old wizard giving exposition is probably telling the truth, but we're forced to take him at his word) - I would have liked to have seen either some interaction with Luna that suggested the relationship wasn't working, or some better justification for why the heart is able to make the prediction it does.
The pacing of the whole second half feels very rushed, which might be a word limit thing - basically everything after leaving the Crystal Kingdom (Empire?) feels like it's trying to tick the necessary checkboxes to set up the conclusion.
I did like the Star Swirl characterization at the beginning, and the concept here is interesting, but on the whole it doesn't quite land.

I pretty much agree with >>Baal Bunny. There are plenty of solid lines, but there's not really a plot as such, and "parallel universe except they're dogs" isn't quite enough to hang a story on.
Dash/Lash didn't feel against type to me - she's not arguing against adventures, just pointing out that lots of adventures are already happening.
Is there a wordplay I'm missing with respect to Rovera's name? All the other names seem to be referencing their pony equivalents, so I assume there is, but I can't figure out what it would be.

In addition to the above, I was a bit thrown by the repeated mentions of hunger/tiredness - it seemed like you were setting something up with those and the decision to enter the cavern in search of food, but as soon as they spot the gem that thread just sort of disappears. Not sure if it was meant to be a thematic commentary of some sort - if so, it went over my head.

Rereading this before commenting, the "antique toothpick" line remains fantastic.
I disagree pretty strongly with >>Baal Bunny regarding the opening paragraph - it's true that the scene-setting at the opening isn't terribly efficient plot-wise, but this story is fundamentally a shaggy dog joke, and those don't really want to be efficient. Besides, the story really needs to set a dramatic tone in order to subvert it later, and the opening felt to me like it did that very well.
I think I agree with Chris about the gallows line - it's not necessarily unreasonable for a darker take on Equestria to involve the death penalty, which isn't substantively all that different from the semi-permanent petrifications we see in canon (and I do think, given the basic structure of 'set up dramatic situation, then subvert it hard for a punchline', that it makes sense to suggest a somewhat darker take on Equestria than the default assumption), but I did find myself spending more time arguing with myself about whether Equestria would have gallows than I think is desired. That said, while the line stuck out on reread, I don't remember noticing it much on initial readthrough, so I might just be being over-influenced by Chris's comment.
The perspective shift felt fine to me - from Rarity's perspective this is a horror-drama, and from Fluttershy's perspective this is a comedy, so lining up the perspective change with the genre change seems reasonably natural. I actually think doing this all from Fluttershy's perspective would weaken it somewhat, since then the pulling of the rug would feel much more like authorial sleight-of-hand than it currently does, which would take focus off the absurdity of the situation.

I love the use of colors in this one - the way the dogs seem to loom out of the shadows and the brightness of Rover's eyes against the duller colors of everything else both give a very eerie atmosphere.

This is fantastically cool, and I wish I knew enough about art to say something more intelligent about it. I love the sense of motion, the slightly uncomfortable elongation of the ponies, and the way you did the layers on the heart, but there's also something about the composition that makes it more than the sum of its parts, and I wish I could put a finger on what.