These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Complete Monster: Liliana is very heavily implied to be one. She took part in numerous acts of mass murder as a member of the Purist Faction (and enjoyed them all), displays an obvious lust for violence and destruction, and transitioned to the Black Knights largely to satisfy said bloodlust. Come to think of it, she's Luciano, only female and technically working for the good guys.
Luciano is as well, just like in canon.
General Cao, even though he was a posthumous character. He blackmailed Rakshata into creating four powerful knightmares by threatening to massacre Mumbai. She did this....and he slaughtered the city anyway, causing this AU's Rape of Nanking. Why? To "remind her of her place." Even the Britannians were disgusted by the sheer level of depravity involved. When Xingke learned the truth, he was ashamed and disgusted that his former country not only allowed it, but gave Cao a free pass on his actions, such that they sealed all records of Mumbai afterward.
As this is the same General Cao that led the invasion of Kyushu, it's darkly hinted that this could have been Japan's fate had the Chinese Federation succeeded in wrestling it away from Britannia.
Crowning Music of Awesome: Cataclysm Over Paris being played over the recently decimated Pearl harbor followed by Zero's speech was pure eargasm.
Darkness-Induced Audience Apathy: It really happens as one reviewer put it: "It's just getting a little hard to believe that their world is actually worth saving and stuff."
Technically speaking, Lelouch has claimed time and again that he's not out to save the world, but to destroy it and replace it with something better. In that regard, kind of pointless to destroy a world where there's only one evil empire as opposed to one made almost entirely up of tyrants and their warring legions.
Ethnic Scrappy: Zulfiqar, which a few have seen as a stereotypical depiction of Arabs and Muslims in general; one reader from Pakistan even claimed the author as racist over it. The author has since put out a note that explains Zulfiqar is only representative of Islam's radical element, not the whole.
Hilarious in Hindsight: Suzaku's reason for killing his father (to keep him from killing Lelouch and Nunnally) inadvertantly draws in part from the Code Geass light novels rather than the anime.
Jerk Ass Woobie: Cornelia. She's arrogant, and can be nasty. On the other hand, the scene where she's confessing to Guilford about how she never got to apologize to Euphy for insulting her and her ideals (their very last coversation was Cornelia calling her an idiot for throwing her title away for "worthless ideals") is downright heartbreaking, and she's now a broken shell of a woman.
Magnificent Bastard: Along with Lelouch and Schneizel, there's also the trope namer Erwin Rommel.
Mexicans Love Speedy Gonzales: Despite the Nazi references, the story has a fair amount of German readers who actually enjoy the depiction of a Third Reich-styled EU, alongside the likes of the Afrika Korps and Rommel. The only common complaint is the author's horrible attempts at writing their language.
Also fits C.C.'s prayer, which several French readers have commented positively on. Same complaint though.
Narm Charm: Seeing Marianne taking over the mind of a lieutenant to have a talk with Anya. Her, talking in a high-pitched voice while possessing the body of a random mook may seem to be a good opportunity for a laugh. BUT IT'S NOT!
Tear Jerker: Cornelia's confession to Guilford about how she never got to apologize to Euphie for yelling at her in their last conversation. Much as a bitch as Cornelia is, it's hard not to feel sorry for her, given how broken she's become.
What an Idiot: A few factions believe that they can control Lelouch/Zero (depending on whether or not they know they're the same person) for their own ends... ... ... ... HA.