Well... if someone's still interested, I think these two count as part of the theme.

Human

In Equestria's far future, one thousand and five years after the return, a dysfunctional group of argumentative ponies must quest to defeat the most dangerous enemy of Equestria to ever live; the malevolent Lord Second, one of the only known members of the race of elder gods known as the humans, and the ancient cult who worships him, the Brotherhood of Man.

Human:Shades of grey

Not so long ago, Equestria barely defeated two almost unstoppable creatures known as humans, which they called the Second and the First. Almost five years later, another one has shown up. The military takes up arms, the princesses are stricken with fear, and the Elements of Harmony assemble, ready for battle. But 'the Third' has no idea what's going on, and only wants to know how he came to be here, and how to get back home. Good questions indeed...But will he ever get his answers? Or will his predecessors' legacy catch up to him first?

In both of them, humans seem to posses "Meta-powers" and "Meta-physiology", effectively making them alien to the "inherent" rules of their universe, and granting them the ability to control, alter or exploit the "laws of physics" and "causality".

In a minor example (only speculated).

Diary of a store clerk
The MC shows biological anomalies that, curiously, would serve or seem in place, in the creature he "claims" to be.

Day one

A man is transported to Equestria through some unknown means. Instead of becoming the life of the party in an instant, he is forced to survive using less than conventional means, hiding from the denizens of Ponyville in fear of how they would react to a human being. But such an existence cannot last forever.

As well, he must contend with the reality of an incomplete cartoon world. Things are not as easy to adjust to as they seem.

In this one, the human notices "inconsistencies" in the ponies "world", and how the universe reacts to him.
Don't expect a good ending.

Death becomes her

The Gates of Tartarus have been breached, releasing evils long since vanquished back into Equestria.

Celestia sends her student Twilight Sparkle to investigate the Gates of Tartarus, but when things don't go quite as planned the young unicorn is forced into a difficult position. Through blood and tears she will be tested harshly, both physically and mentally. With unparalleled strength of self and unwavering faith in her princesses, Twilight takes up a mantle that no pony should ever be forced to bear.

The human is kind of an 'old' god, there have been few scenes involving him, put this because of this quote in chapter 6:

“You feel cold because you think you should, you think the laws of the world apply to you.”

May be foreshadowing for something.

Anyone still here?

Anyways, new story: Not the hero

Discord's the only creature in Equestria who can recognize the human for what he is -- not the long-lost Seventh Element that never actually existed and couldn't have existed before the human arrived, but a meta-reality warper, an entity far more powerful than Discord with the power to warp the minds of all around him and the very rules of magic to make sure that he's always the Big Hero.

Pretty self explanatory, a Human-ish concept with obvious differences, the human does not seem to get his powers as if (or because) he is in a "toon world" as a character. But rather as a subconscious reality warper.

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So basically, a Gary Stu, but Discord is somewhat immune and aware that this is all happening. Nice.

Also hi, new to the group, long time author that hasn't been here in a while. Anyways, while this is going on, I'd thought I drop one too.

The Monster Mash by FredMSloniker
The Monster Mash
The only thing is that I recommend a HaC story is the Twilight one. In it, Twilight finds an old tome belonging to a wandering pony. She doesn't know it, but there are some things that ponies were not meant to know.