@Eclipse  
Darkstalker Sombra:Your ancestor claimed the Dark Soul and waited for Fire to subside.  
And soon, the flames did fade, and only Dark remained.  
Thus began the age of ponies, the Age of Dark.
 
King seeker Moochick:  
Those who seek the Realm of the Lords must brave Niblick’s Fortress, a deadly house of traps.  
Many have gone before you, but none have returned.  
Fate has chosen you, but proceed with caution.

In the Age of Chaos, the world was unformed, shrouded by fog.  
A land of white crags, worldtrees, and everlasting draconequus.
 
But then there was Fire. And with Fire came Disparity.  
Heat and cold, life and death, and of course…Light and Dark.
 
Then, from the Dark, They came.  
And found the Souls of Lords within the flame.
 
Smooze, the first Demon.  
The Witch Hydia and her two daughters, Reeka and Draggle.  
Tirek, the Lord of Tartarus, and his faithful dragons  
And the first pony Faust, so easily forgotten.
 
With the Strength of Lords, they challenged the draconequus.
 
Tirek’s Rainbow of Darkness peeled apart their twisting flesh.  
The witches weaved great magi-storms.  
Smooze unleashed a torrent of it’s own putrid self.  
And Discord the Mad betrayed his own, and the draconequus were no more.
 
Thus began the Age of Fire.
 
But soon, the flames will fade, and only Dark will remain.
 
Even now, there are only embers, and pony sees not light, but only endless nights.  
And amongst the living are seen, carriers of the accursed Darkmark.

@JAKKandJING
 
True, but that doesn’t exclude him from being the Pygmy. Stay with me here:
 
Manus is referenced over and over again as being “the primeval human”. Who would the primeval human be if not the one who split the Dark Soul and scattered it’s pieces(Humanity) to create mankind?
 
Not only that, but he is the “Father of the Abyss”. The Abyss is the primordial darkness, the oppositon to the primordial flame, or the First Flame. Again, the best candidate for the title of Father of the Abyss would be that first being who found his soul in the Dark.
 
Then, there’s the whole (murky) subject of the Pendants. Originally, the Pendant starting item was intended to be a relic passed down through mankind all the way from the Furtive Pygmy himself. The Broken Pendant found in Duke’s Archives is somewhat of a callback to this. Not only that, but it is explicitly stated that Manus has a burning desire to be reunited with the Pendant, so much that he reaches across TIME AND SPACE to fetch it(and you). If that is not Lord-Tier power, I don’t know what it is.
 
True enough, we have the fact that Manus doesn’t look like the Furtive Pygmy in the intro. But that is rather easily explained. All Lords began as genderless humanoid figures, remember? Only after acquiring the Lord Souls did the Lords take the forms that they carried through to the game. Same goes for the Pygmy, since we never see his “final form” in the intro.
 
There’s also a theory about why Manus’ humanity(that is, his soul. After all, his soul is described as being “a lump of humanity”, further lending credibility to his identity) went wild.  
Simply put, because he was brough back from the dead. Ressurection seems quite the traumatic experience in Dark Souls, what with the Hollowing and all. Something akin to this could have happened to Manus, making him lose his marbles.
 
 
Again, I’m not saying that Manus is the Pygmy and you should shut up because my opinions on the Internet are better than yours. There’s still the probability that he isn’t. But there’s also a chance that he is. One can never be too sure with Dark Souls lore.

@Ghouleh
 
However, It is mentioned that Manus became what he is when the humanity within him went “wild”.

@JAKKandJING
 
No.  
Actually, your theory is as good as any. But there is good evidence that Manus is the Pygmy. One can never be too sure with Dark Souls.

@Ghouleh
 
Actually, the furtive pigmy passed part of the dark soul through his bloodline in hopes an ancestor would put out the first flame.
 
Manus is father of the abyss and he was a normal person before that.

…damn. That catches the scene perfectly.  
The “primeval pony”… Father of the Abyss.

“And the Furtive Alicorn, so easily forgotten.”