Base Breaker: The military adviser Julius Kingsley turns out to have been a Lelouch brainwashed by Emperor Charles to do his bidding before he sent back to Ashford Academy with Rolo. While some people were happy to see him even before his identity was confirmed, others were less happy about his significance in the story, having felt that he might have overshadowed the main cast a little too much.
Broken Base: Early into the OVA, the Code Geass fandom became divided over Akito for different reasons. Some preferred to see the original cast back instead of the new characters, while another faction was glad to see a different side of the fictional universe and quickly warmied up to the changes. Others didn't like how the overall tone of Akito is far darker than even the first season of Code Geass, which appeals to the tastes of certain viewers who thought the original show was too goofy, but not necessarily everyone else. On the other hand, the brief appearance of Suzaku and "Julius Kingsley"/Lelouch in the second chapter was also divisive, with some welcoming this turn of events because they missed seeing familiar faces or at least felt it would make the situation more interesting, while others feared the risks of reusing characters and concepts from the main series. As it turned out; Suzaku and Lelouch do get some decent screentime, but the main focus is still on the new cast.
The ending has also been rather divisive; besides the arguments about whether it was rushed and/or too happy, one of the biggest disputes revolves around the sudden increase in the inclusion of supernatural elements, and whether they fit the show or were simply hamfistedly shoehorned in.
Crazy Awesome: The second episode has Akito channeling his craziness with his allies to increase their abilities. It's like if Sunrise took notes from this trope.
Darkness-Induced Audience Apathy: The show is very dark, to the point where the differences between the EU and Britannia seem almost minimal. Which, along with the other reasons mentioned in this page and the fact that the EU ends up being defeated in R2, may possibly make it hard to care too much about what happens in the series. That said, later episodes do bring back some of the idealism and even lightheartedness that were also present in the original show.
Funny Moments: Ryou's facial recognition profile for his pirated Knightmare lists him as General Napoleon Bonaparte, with a birthdate of August 15, 1769, and 9's filled in for everything else (Height: 999, Weight: 999, ID: 99999999, etc.).
Narm: The ridiculous amount of racism in the first episode: if there's a chance for a European character who's not Leila to be racist, they will usually try to take it. It's a bit overblown, at least compared to the original series.
For example, when Akito threatens a person by employing a racist claim about how good his people are with sharp objects, although it later turns out he was actually half-joking.
Reality Is Unrealistic: The treatment that the Japanese have is based on the real phenomenon of Displaced Persons or DPs. Some of the biggest waves occurred after World War 2 and cause considerable friction to this day, however to younger generations the phenomenon isn't as well known. That said, Akito the Exiled takes the concept and drums it Up to Eleven. Only in Code Geass is it politically correct to use DPs as kamikaze units (not to mention sacrificing high tech military equipment along with them), as well as go through the full Ghetto treatment even in the resident Federation. Thankfully latter episodes play this down considerably.
Additional Narm comes from the scene in episode one where Akito shows his military ID to that one truck driver. Previously, the truck driver had treated him like a fellow EU soldier, but afterwards he looked upon him in disgust. And that's before Fridge Logic sets in: shouldn't the truck driver have recognized Akito as Japanese up front by his facial features? Perhaps he initially thought Akito belonged to another Asian ethnic group instead, but this isn't made clear.
That said, the overblown racism seems to be deliberately invoked, as the European elite seem to encourage anti-Japanese discrimination at least partly to allow them to exploit an ever-replenishing supply of cannon-fodder, since they couldn't sell an otherwise stagnant and unpopular war to the general public.
Some of the angry Torches and Pitchforks rioters in the third episode look kind of funny. In addition, their apparent readiness to go that far so quickly is also somewhat amusing to see.
Akito's Geass makes him and anyone it spreads to scream "DIE" over and over.
Shin Hyuga Shing's Knightmare, Vercingetorix, is a mixed bag, if not for how extravagant it is. The axe is way too intricate (most of it being clock gears stacked on top of each other in a physically impossible manner) and yet it rips apart Akito's Alexander just fine. Additionally, he enters into the fight in its centaur mode, with the mech's golden plating making it all the more jarring. That said, the knightmare actually looks very intimidating, while the centaur mode is actually practical (considering its sheer mobility).Overall not something you'd want to run across in a battlefield.
Seeing Lelouch/Julius Kingsley putting a crazy plan into action again as a would-be Rabble Rouser who stirs up the European masses. The outcome might feel exaggerated in terms of more or less stretching the viewer's logic, but that over-the-top nature is one of the elements people enjoyed about Zero's plans, regardless of just how unrealistic several of them turned out to be.
Unintentionally Unsympathetic: The main characters (minus Leila) initially fall into some of this (and even Designated Hero) in the early episodes. The titular protagonist is Ax-Crazy in battle and kills enemy pilots quite ruthlessly, while the other three Japanese characters are criminals: one even blew up a building with students still inside, which despite his Freudian Excuse was a bit excessive. Overall, this might be considered the largely inevitable consequence of creating a Crapsack World setting, but it could also be hard to root for the good guys at times early on, especially when many of those running Euro Britannia are surprisingly honorable. That said, the main heroes all eventually mellow out considerably.