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.
Alternative Character Interpretation: XANA, because little is actually established about him/her/it, can be translated anywhere from misunderstood, going for some vague goal in its programming, bugged, to a complete monster. XANA might have gone insane from the horrors of humanity. This explains it further around 12 paragraphs in.
Copy Cat Sue: The fanfiction. Good luck trying to find a story without an OC going/knowing about Lyoko or some event that leads Yumi and Ulrich to confess their love for the other.
The theme song, despite having cheesy lyrics, is extremely catchy. Worth noting is that it's a lot less cheesy in French as opposed to English. Both versions are total Ear Worms, though. However, translated, the two versions pretty much mean the same thing. The French version is actually a lot more repetitive.
"XANA Attacks!" is the ominous and oppressive-sounding leitmotif of the Big Bad in the series that signifies when things are getting dangerous, and the melody appears in other fast paced battle themes like "XANA's Monsters" and "Facebook Battle 2".
William was despised by most fans for getting in the way of Ulrich and Yumi's relationship (not thattheyneededthe help). A few defected after Season 4, but he is still largely a disliked character.
Also Sissi for some in the Fan Dumb, even though she was barely ever a threat to said Ship. To be fair to these fans, the writers DID give Ulrich and Sissi some pretty big damn kisses in "Frontier" and "Ultimatum", all the while cutting Yumi and Ulrich's kiss short in "Routine".
Theo Gautier, a one-shot character who displayed interest toward Sissi then toward Yumi, is either used to get Sissi out of the way while averting this trope, or portrayed as a Jerkass and abusive boyfriend toward Yumi so she can run into Ulrich's arms (despite the fact he is even less of a threat than Sissi is).
In "Code:Earth", Yumi is trying to get her parents to agree to letting Aelita stay at their house. When they ask what her parents do, Yumi makes up on the spot that they "work with computers". And who should have created the supercomputer other than Aelita's father, Franz Hopper!
When William finds out about Lyoko in "The Secret", Jérémie calms down Ulrich by saying they just make him forget with a Return to the past. William, not understanding what they are talking about, answers he never forgets anything. We later find out he indeed remembered this episode's events even after the Return to the Past, though only as a dream.
Hollywood Pudgy: In "Tip-Top Shape", Sissi is told by the nurse that she's 5 pounds overweight, but she's just as skinny as always. (The scale read 110.7 lb [50 kg]. If she was 5 pounds overweight she'd have to be 4'7" [137 cm], but she is a bit taller than Ulrich who is 5'1 [156 cm].) Lampshaded by Aelita.
Ho Yay: Some of the more notable examples include:
"Triple Trouble" — After Jérémie tells Odd that he's developed a new power for him on Lyoko, Odd says, "You're the best, Einstein! If you were a girl, I'd propose to you immediately!"
"Replika" — Nicolas initially asks Aelita if she'd like to go on a "fantastic and breathtaking experience in the moonlight". She ends up pulling out, so instead Nicolas ends up spending the night with... Hervé.
Idiot Plot: The show stresses The Masquerade, yet the gang has openly mentioned Lyoko and XANA within crowded areas talking louder than anyone else as well as in front of at least one person not privy to the secret — and somehow this generally doesn't expose them all. This has actually happened at least 20 times within the first two seasons alone. Mitigated, of course, by the Reset Button — but the point still stands, as they're way too much relying on it to cover their indiscretions. They also often pass it off as discussing some movie or video game.
Jerkass Woobie: Sissi on several occasions, particularly during XANA attacks and especially after the prequel reveals that a stupid misunderstanding and Ulrich's hurt feelings contributed to Sissi being a Jerkass to begin with; otherwise, she's kind of nice.
Lost in Medias Res: One thing that hurt the show's rep in season one. While it gives the show some mystique and encouraged some to keep watching, for others, they were confused.
Starting around mid-season 1, Sissi and Jim got much more noble moments and even some awesome ones, and they became mostly very well-liked. Jim also started to become a bit more humorous as time went on, as seen in Season 2 when he started using his "I'd rather not talk about it" catchphrase.
To a lesser extent, William was also rescued from the heap when he become The Dragon to XANA, since Evil Is Cool.
Ron the Death Eater: The treatment that Jérémie gets from a lot of Odd×Aelita supporters in fanfiction. Good luck finding Oddlita fanfiction that doesn't feature Jérémie as physically, verbally, emotionally, or sexually abusive towards Aelita.
Seasonal Rot: Season 3 is often considered this. Among other things, it was only half as long as other seasons, Yumi's Designated Victim status became exaggerated, the tone was Darker and Edgier than even season 2 (and, by contrast, the comic relief became less funny, especially when it involved the usually-reliable Jim), and also the huge potential after the season 3 finale never came to fruition when season 4 arrived. Season 4, while a step up from Season 3, also gets flak for being too long with too much Padding and boring Filler episodes, and generally not reaching the heights Season 2 did.
Ship Mates: Most shippers that support Ulrich×Yumi also support Jérémie×Aelita, and vice versa. Those same shippers will generally ship Odd with either Sam (a one-shot girlfriend of his) or Sissi (a frequent subject of Ship Tease with him).
Squick: In the novel series, Odd falls for a girl named Eva. And Eva is XANA.
News of the new project ("Evolution") being live-action is already being met with fervent hatred in some places. Even fans who are willing to give the show a chance have expressed doubts about this change.
The novels have also been criticized for taking huge liberties on the source material.
They Wasted a Perfectly Good Plot: Season 4 is seen as mostly a missed opportunity amongst the fanbase due to the plot getting shafted for Filler throughout a majority of the season when it could have been used to further the exploration into the digital sea or digging deeper into XANA's Lyoko replicas. The sudden, out-of-nowhere, series ending didn't help matters either.
Viewer Gender Confusion: Odd has often been mistaken for a female. Even more so in the French dub, due to his voice.
Aelita. Big time. When the character ends up almost Driven to Suicide, you know it's bad.
Also, to an extent, William at the end of the show. Poor guy spent entire month as a Brainwashed and Crazy minion for a malevolent IA, fighting the very people he wanted to help (including the girl he is in love with), and when he attempts to redeem himself, the Lyoko-warriors, feeling still uncomfortable about the time they were fighting him, reject him.