Ascended Extra: A great deal of minor characters have their roles expanded, compared to their appearances in Code Geass proper. For example, Senba, previously little more than a Living Prop with a voice in the show, is now something of a Parental Substitute and mentor for Tohdoh.
Colour Coded Armies: Though a minor detail, the various factions (beside Zulfiqar and the Order) in Megiddo appear to follow a color system, with the uniforms and/or standard knightmares and ships of each faction holding a theme color. They are laid out as so:
Did You Just Talk Down To Cthulhu!?: A month or so after the Devastation, Milly and the rest of the Ashford Academy survivors are brought before Emperor Charles so that he can Geass away their memories of Lelouch and Nunnally. This is what happens when Milly was ordered to kneel: rather than cower before the Emperor like most would do, Milly, being too pissed over recent events to care, summarily calls Charles out over Japan's destruction and Britannia's callousness, as well as openly declare that she (in the same light as Lelouch before her) would destroy Britannia if she had the power to do so. Naturally, everyone expects Milly to die for this offense; instead, Charles laughs it off and praises her spirit, right before declaring her as the new Duchess of New York (her grandfather's old title) and returning all holdings the Ashford family had lost over Marianne's death. That being said though, Charles still Geasses her and the other students.
Even Evil Has Standards: Some Britannian characters display signs of this. For example, Charles holds certain contempt for Britannia, which he considers an empty and meaningless nation; in fact, the only reason he retains the throne is because it benefits Ragnarok. Otherwise he would have given it up to Schneizel a long time ago.
Luciano, like the other Rounds, is greatly disgusted with Descartes and his Smug Snake attitude.
Calares is a Grade-A son of a bitch who practices all the things that make Britannia evil, but even he looks down upon the Eunuchs for their hedonism and their being traitors. In fact, he lampshades it noting while it's one thing for Britannia to subjugate other nations, it's another for the leaders to do the same to their own and then sell it out at the first opportunity.
Expy: Played with. While Rommel remains the same personality wise, he seems to be a lookalike of Ali al Saachez.
Seems to be a thing with some of the OCs. Zhukov and his son, as described, look like Sergei and Andrei Smirnov, Yamamoto sounds like Gendo Ikari, and Nagumo, Yamaguchi and Kondo strike one as being based on Aokiji, Kizaru and Akainu.
Obviously, Knights of the Round Johann Ernst, Michael Raleigh, Nena Gurlukovich and Descartes Castin are each based on certain 00 characters.
Not exactly a character expy, but the new Black Knight uniforms are essentially black and silver clones of the A-Laws uniform, with commissar caps and assorted rank/unit insignia thrown in to make them even more Badass. Their knightmare pilot suits are also based on the A-Laws' normal suit (pilot suit), but are black instead of green.
Same goes for the EU and Chinese Federation pilot suits, which are now respectively based on the Orb and ZAFT normal suits from Mobile Suit Gundam SEED Destiny. Britannia still retains their original designs though.
And since we're on the subject, the CLA uniforms are expies of ZAFT wear, only with the following changes. The standard uniforms are colored dark red, those worn by Xingke's followers (the Tianshou Team) are gold and Xingke himself wears purple (which is the uniform color of the CLA's upper brass in general). Beyond that, the ZAFT insignia are also replaced with the Chinese Sun (the emblem on the Chinese Federation flag).
The author has commented that he uses expies (at least in terms of appearance) because his readers are more likely to recognize/visualize them than completely original characters.
Freudian Excuse: Rikichi has a surprisingly compelling one. His parents had to work hard to be recognized as Honorary Britannians (read they had to practically debase themselves) and even when they succeeded they were still stepped on; they couldn't even report a robbery of their home simply because they knew the police wouldn't give a damn. The Devastation didn't exactly help matters either.
In-Series Nickname: Though they still have genitalia, the High Eunuchs are (mockingly) regarded by their namesake because they elected a then extremely young Tianzi to the Chinese Federal Chairmanship to serve as their puppet leader, causing the regular populace to compare them to the villainous Eunuchs of the Han Dynasty. This naturally resulted in Disproportionate Retribution, namely in the form of clampdowns by the Federation's Secret Police.
Mugging the Monsters: This is what happens when a bunch of Chinese secret policemen attempt to rustle up a pair of harmless looking old men who turn out to be Setsuna and his fellow shinobi Yukihiro Sanada.
Noodle Incident: Due to the fact the entire Old World seems to be at war, lots of battles happen offscreen; the Britannians seemed to have suffered a heavy blow at the Rhineland, for example.
No One Gets Left Behind: The Britannians in the Black Knights show what happens when people don't play this trope straight.
Not only the military, but also the entire Ashford Academy student body, including Milly, Rivalz and Shirley.
No Swastikas: Averted. The insignia of the Black Knights' Security Corps is a silver manji.
Oh Crap: Lelouch's reaction upon seeing Johann in China, since the latter is a Worthy Opponent (the only other person besides Schneizel to beat Lelouch in Chess) and Lelouch wasn't expecting one that time around.
Overpressure? What Overpressure?: Averted. Lelouch orders the Ikaruga to fire Raikou missiles into the ocean, thus causing an underwater explosion that promptly destroys the Britannian submarines in proximity with the change in the pressure.
Paint It Black: Literally, in the case of the Black Knights' knightmares and ships.
Posthumous Character: Genbu Kururugi, who is long dead but appears frequently as a hallucination(?) to Suzaku.
Putting on the Reich: The EU uniforms are very Nazi-like (right down to the emphasis on grey), for obvious reasons.
The Quisling: Descartes for France and the Eunuchs for China.
Racist Grandpa: Rikichi's hypocritical racism is due to his grandfather.
Rape Is a Special Kind of Evil: Out of all the Eunuchs, Zhao Hao is especially hated by Calares and his staff because he's a pedophile. In fact, he once tried to force himself on a younger Tianzi, only to get his arms cut off by Xingke for the effort.
Red China: As opposed to the Romance of the Three Kingdoms knock off it was in R2, Megiddo's depiction of the Chinese Federation was pretty much a copy of the real life PRC. It's since been annexed by Britannia due to the Eunuchs' treachery.
Shown Their Work: The author has provided a lot of information about the mechas with a high level of detail in his wikia.
However, his use of plushies of Godzilla and company in one chapter is wildly inaccurate. Although the alternate timeline of Code Geass is supposedly set in the relatively proper time period for Godzilla and co. to have appeared in at least a few movies from the showa era, the fact that nuclear weaponry apparently does not exist until Nina creates an equivalent version in the form of FLEIJA means that in this world Godzilla, Mothra, Rodan, King Ghidorah and Anguirus, who all appear as plushies at one point owned by the children of Ohgi and Villetta shouldn't exist either. Why? Simply put: There was no Hydrogen bomb to set events in motion that would inspire the creation of Godzilla and his cohorts in Code Geass. Their appearance in this fic is therefore an anachronism.
Even so, Godzilla and Jet Jaguar figures (or at least close lookalikes) are clearly shown in episode 5 of season one around one of the graves Suzaku and Euphie visit, which means that Kaiju Eiga exist in the CG universe. Also, one should note that of the aforementioned monsters, only Godzilla and possibly Anguirus were created with nuclear weapons in OTL, whereas Mothra was the guardian spirit of Earth, the Rodans (there were originally two) were pterodactyls that went into slumber eons ago only to be awakened by excessive mining, and King Ghidorah was originally an alien monster before being retconned in the Heisei era. Following that, as Code Geass is set in an Alternate Universe (as mentioned), one would believe there are plenty of ways for Kaiju Eiga to come into being and circulation without atomic bombings serving as a backdrop.
Shut Up, Hannibal! - Milly invokes this trope in the Word Dramas when Suzaku tries to talk her down from blasting Charles (holy shit) over the Devastation.
Sociopathic Soldier: Liliana is implied to have been one. Luciano definately is, while Rikichi may also qualify.
State Sec: The Black Knights' Shinobi Corps acts this way, overseeing Internal Affairs within Okinawa and the "regular" Black Knights as well as performing black operations in the outside world to ensure Okinawa remaining secret and forgotten. Needless to say, the other Black Knights have mixed feelings about them.
And then there's the trope namer Schutzstaffel, which are fittingly the EU's force.
Especially Kallen, which only makes sense since C.C. gave her Geass.
Even Lelouch has gone up a few levels, as he can hold his own against Suzaku now. All thanks to Bismarck training him.
Alfred also gets a mention, as he was able to fight Guilford and beat him, albeit with a Bigger Stick. I doubt he could have done that in canon.
Two Decades Behind: As in canon, the CLA is highly antiquated in both technology and training; the only real advanced tech they have are the Shen Hu and its three sister units, while Xingke and the Tianshou triplets are the only highly skilled soldiers/pilots. This is emphasized several times as the reason the CLA hasn't made any headway in living up to its name for the last seven years.
Britannia is this when compared to canon. Even though eight years have passed since season one, the only next generation knightmare they've produced is the Vincentnote which Cornelia pilots instead of Rolo. The explanation is that the Ashford Underground has executed several sabotage operations in Britannia's corporate and industrial sectors, which has kept production of the Vincent derivatives back for several years (and may have also forestalled the Gareth and the Lancelot Albion as well).
Ultimate Job Security: Rikichi may qualify because of his racists views, the fact that even his teammates reject him and his skills on a knightmare are pretty much Informed Ability when he's not shooting disabled knightmares. Yet, he's still on Zero Squadron.
In Rikichi's defense, he has only been depicted in a few battles thus far (in which he has done a lot more than shoot disabled knightmares), and the one he got his ass handed to him on was against Gino, who later fought Kallen to a standstill (at least until she activated her Geass). Otherwise, yeah he should have been let go a long time ago, but when you have low manpower reserves...
This is lampshaded by Alfred and a few other Zero Squadron members early on, who question Kallen on why she took Rikichi into the squadron despite the aforementioned (Kidomaru even remarks he could be trouble in the future). For what it's worth, Kallen's explanation was that he did his job and he followed (her) orders.
This was later noticed by Kallen and thankfully averted.
World War II: The story is filled with references (some more obvious than others - North Africa and Pearl Harbor), and the current setting seems to be modeled after it.
Most of the EU leadership seems to be ripped right out of the Nazi High Command, and the Union itself is German-dominated. For example, Joseph Goebbels is the President and Reinhard Heydrich is Kriegsfuhrer-SS.
And let's not forget the other nations that make up the EU, whose militaries are led by several prominent World War II-era commanders, from Georgy Zhukov to Charles de Gaulle (the latter now renamed Gerard, likely to avoid confusion with Emperor Chuck).
The Black Knights High Command is composed of lead commanders and military figures from both sides of the real world Pacific Theater. In fact, the only one that seems to be missing is Nimitz!
Bernard Montgomery and the infamous Operation Market Garden have just been mentioned as well, alongside Bradley, Eisenhower and Patton. All Britannians of course.
In the latest chapter, Rikichi has an internal monologue where he details his desire for power, alongside his plans to implement a Holocaust-esque program against all Britannians in Japan and to purge the Black Knights of all Britannians and half-Britannians (aside from Kallen of course). Also, Rikichi is in the process of writing a book called "My Fight". Which, translates to German as Mein Kampf.
The book title has since been retconned to Hitoritabi, or "Solitary Journey", but the theme still remains.