Alternate Universe: The Equestria in this fic is decidedly non-canon, as to allow the author a little more leeway in characterization and creating a geography for the wider world(s).
Assimilation Plot: While this is a stated goal of those who believe in the Conversion Movement, as it is later known, Celestia and Luna intentionally slow walk things; to the point where most of the public remain unmoved to Convert mostly out of apathy.
Blue with Shock: The Mane Six, Spike, and the Royal Sister's reaction to Midori Hana when she first arrived in Equestria, and deigned to speak about inanimate objects suddenly engaged in song and dance.
Color-Coded Wizardry: All Terran Magic has a signature color: Blue Water, Red Fire, Green Earth, Gold Wind. When the 'Mixed' Elements are found, they follow the same pattern: Periwinkle Lightning, Aquamarine Ice, Forest Green Wood, Silver Metal, White Light, and Dark Violet Shadow
Played straight with the Conduits of Terra — Blue Vague (vague is french for waves of water), Red Blaze, Midori Hana (Japanese for Green Flowers, although her element is Earth), and Golden Storm
Averted somewhat with the Mane Six when they find their own Terran Magic: Applejack gripes that the dark green runes of Wood Magic clashed violently with her orange coat, and aquamarine doesn't exactly mesh with butter yellow at first blush.
Cybernetics Eat Your Soul: Largely averted. While almost everyone not explicitly in a desperately poor country have cybernetic implants, they mostly show no ill-effects of it. The more extant danger to the soul is the absolute lack of a creative outlet, aside from trying desperately to be noticed and recognized on the World Wide Web.
Gaia's Lament: This in spades. Few if any dare set foot out of a city not because of some law or extant danger, but because over-industrialization has made anywhere not settled by humans eerily quiet and dreadfully boring. This leads to most Converts being completely floored by Equestria live and in person, mostly because the whole world doesn't seem like a neutral-color abusing, prefabricated cut-out.
Midori Hana: It's like everything is alive. Even the things that should be inanimate, like the houses and the stone roads, just feel... alive somehow. Like if everything were to suddenly get up and start dancing then it would not be entirely out of the ordinary here.
Green Aesop: While not stated explicitly (too much), The author does make it a point to state exactly why the Earth is so damaged and where this batch of humans screwed up.
Our Souls Are Different: All sentient creatures carry a Spark, which is effectively a Soul and all the retained memories of the being that possesses it. Conversion generally results in a fusion of the old Human soul and new Pony soul into a gestalt being.
This is Played for Drama with the Four Conduits, as they have to overcome a "Trial of the Soul" involving directly confronting their greatest fear, which is directly tied into to their prospective element. This has to be done since the Shard of Terran Power makes the fusion of their Human and Pony Sparks impossible until the internal issues are reconciled.
Although they could refuse the trail, but that would result in the Shard being lost to that person forever, and their Human Soul effectively blanked out; resulting in a Pony 'born' with no human memories at all. If they accepted the trail but failed, their souls would be been rent into nothingness.
Rockers Smash Guitars: Combined with Improbable Weaponuser, an incident during a Winter Moon Celebration (effectively New Year's Eve) afterparty involving quite drunk Mane Six and Four Conduits ended with Golden Storm wearing a toy guitar over his head, courtesy of Applejack.
The Magic Comes Back: Once all Four Conduits for the four elements of Terran Magic are found, the Will Of The Earth itself states this as their main objective, to unlock the seal placed upon Terran Magic. Seeing how devastated Earth is first-hand, the Mane Six and the Princesses agree, and help train the Conduits to that end.
Small Secluded World: Many of the so-called Elites have walled themselves into nigh-impenetrable domed cities, and have virtually walled themselves into their own version of the internet.
Sugar Bowl: Averted somewhat with AU Equestria. It is better than Earth only because Powers That Be for Equestria are a pair of Alicorns who genuinely want the best for their 'people' and environment, whereas for Earth, they largely stopped caring (or were paid not to care.)
Training from Hell: Due to Luna's rather, out-moded ways, this ends up being how the Four Conduits are trained in both Equestrian Magic and Terran Magic (the latter of which was especially hard to do since to that point in the story ONLY the Conduits could perform Terran Magic at all.)