Affably Evil: Despite being the main antagonists, much of the Aztec pilots are far more sympathetic than Iriana tends to be.
All Nations Are Superpowers: Essentially put, the Aztecs dominate the American continents, while the Iberians control Europe, Africa, and Asia. The Gaia Forces serve as a buffer area, holding the areas around the Bering Strait, much of Oceania, and Australia.
Alphabetical Theme Naming: The 26 Ilivais units have more elaborate titles, but always go by their assigned letter designation. "Ilivais X" is much more convenient to say than "Aztec Ilivais Prototype X- Dark Energy Phonos Weapon", after all.
Animal Motifs: The Avespias are basically bees in the form of building-sized robots.
Animesque: The setting establishes itself with as many anime quirks as possible, essentially so the "dark reprise of all mecha anime" part is more effective.
Arc Words: The quote at the top, used quite a bit by several characters.
Beta Couple: Subverted with Churi and Sycine. They broke up well before the start of the story.
Boring but Practical: The Espadas, while fragile and made in excessive numbers, are quite tactically effective and usable in swarm tactics.
Combining Mecha: The STRUQ Team is this, all of which are awkward-looking in mecha form but much more elegant in part form. Their End Codes have them transform to attack.
Desperation Attack: The End Code, which varies for its users. It's a last-resort move for the GEKICOM Elementals, expending most of their reserves on a single, high-powered attack, unless the unit in question can recharge itself. The Specialized Weapon Units instead just perform a full assault maneuver, though they usually unload all their ammo in the process. In contrast, the STRUQ Team just attack in their transformed components, and can do so at will, and the Phonos Weapons have a Sphere of Destruction that can be used several times.
Elemental Powers: The GEKICOM Team, all of which basically have full control over a certain element. No points for guessing which prototypes compose them.
Expy: A lot, considering that this is a darker reprise of almost every mecha anime ever. The eponymous mech is pretty much Zeorymer (and the GEKICOM Elementals are based off the Hakkeshu as well), many of the characters are incredibly similar to those from other sources, etc.
Foil: Mille and Iriana. While Mille is fairly ample, hot-tempered, reckless, and colorful, Iriana is frail, cold-natured, analytical, and nearly monochrome. Seyne and Iriana count as well: the former usually carries an honorable air on the battlefield and is Weak, but Skilled, the latter is Unskilled, but Strong and often has to resort to playing a bit dirty to win.
High-Pressure Emotion: Deconstructed with the Drive Cores. Whenever someone is resonating highly with their own Drive Core (as in heavily feeling its set emotion), they start to glow and give off huge amounts of energy.
Idiosyncratic Episode Naming: Each chapter is a "day", which makes sense given each one takes place within a rough 24-hour period (though it tends to be more divided on when the main characters sleep). Also, most of the chapter titles not only relate to the specific Monster of the Week, but also somewhat to the character interactions.
La Résistance: The Gaia Forces sorta becomes this, but their intent is to serve as a buffer between the Aztec and Iberian borders, particularly around the Bering Strait.
Loyal Phlebotinum: Subverted. From how Ilivais X "talked" to Mille, it seems as though it doesn't like Iriana that much, as she rejects both the Drive Core within X itself and her own Drive Core that X is coded to accept, but able to pilot simply because she does this. As such, it accepts Mille as its official pilot, which explains why she could use the End Code and instinctually blow stuff up, while Iriana can't use it and she has to struggle to be able to fight at all.
Magnetic Plot Device: Ilivais X, specifically its Cyclic Engine. It's the primary reason the Aztecs don't simply abandon their attacks on Iriana.
Meaningful Name: "Espada" is Spanish for "sword", and indeed, it serves as the basic weapon of the Iberians. "Avespia" is a portmanteau of "avispa" and "espia", or "bee" and "spy", since they have a bee motif and are mostly used for recon. "Oberos" means "to work", as it's a basic labor-type unit. And "Ilivais" is an alternate spelling of "elevais", or "to ascend", fitting since those who possess an Ilivais tend to "ascend" to importance.
Damn near every character's name has some meaning, likely explaining why hardly any of them are anywhere near conventional. We'd be here all day describing what they all mean.
Mini Mecha: The Oberos units, which are unarmed utility mechs the size of a Smart. For being mundane civil service machines, they sure proved effective at the operation to reclaim X.
Real Robot: The Iberian Empire mostly uses the Espada, which is a basic, cheap, but functional weapon that stands at a simple 6 meters tall. The Avespias fall into this as well.
Red Oni, Blue Oni: Mille is the Red Oni (despite having blue-ish hair), as she's more passionate, impulsive, and quite Hot-Blooded. Iriana's the Blue Oni, who at least tries to be calm and composed, but is strung up VERY tightly and prone to completely losing it in all sorts of ways.
Red String of Fate: Iriana did this in a somewhat literal way with Mille, making the string out of each others blood in a kind of haphazard transfusion. Since every cell of Iriana is designed to return to her, this essentially means Mille will always innately know where she is and be drawn to that location.
Sibling Rivalry: Seyne is The Rival to Iriana after all. It may border on an inverted Cain and Abel situation depending on how far Iriana will go, as Seyne's too honorable for that and he believes killing opponents wastes what could be a useful life. This dissipated entirely upon Seyne's Heel-Face Turn.
It's also, to an extent, Iriana's main conflict with the rest of the characters, or even the whole story- in a world that's very idealistic with fairly lighthearted citizens, Iriana drops drama bombs all over the place and overall creates more friction than a centuries-old war.
Square/Cube Law: More or less averted. All the mecha are basically jets with limbs, designed solely for aerial maneuverability. The legs are usually blades or mobile thrusters that could never properly walk, but they aren't meant to in the first place.
Super Prototype: All 26 of the Ilivais prototypes are capable of annihilating entire Iberian armies with ease singlehandedly. A bit subverted in A's case- it doesn't have amenities such as an End Code, wings, or capable weapons, and needs to utilize a lifter jet to practically get around. Seyne just manages to hold his own due to basically being Sanger Zonvolt.
The Phonos Weapons, comprising V through Y, are not intended for mass-production models at all. Their entire purpose is solely to be overpowered, expensive prototypes.
Super Robot: The Aztec Ilivais units are very showy, dynamic, and not very plausible en masse.
Theme Naming: The members of the STRUQ Team have vaguely numerical names in alphabetical unit order- Noille (0), Primo (1), Dia (2), Kolme (3), Lau (4).
Weapon of Choice: The Specialized Weapon Units all make use of a single multi-purpose weapon.
X Makes Anything Cool: Though the use is justified, as it's the 24th prototype out of 26, it can't be coincidence that Ilivais X just happens to have the infinite energy generator and escalating powers and teleportation and regeneration and just a ton of other neat abilities.
Yuri Genre: Doesn't start off having really any subtext at all, but once Mille and Iriana's relationship gets going it becomes quite central to the overall plot.