Konoka acts like a Genius Ditz at first glance, but her excellent academic record, too-flirty-to-be-totally-innocent remarks to Setsuna and masterful handling of berserk Tsundere Anya point to Obfuscating Stupidity. The fact that we've only directly seen her thoughts twice (both for minor things) in the entire series helps.
Negi. Is he a Chaste Hero who cares for his friends and wants to find his father. Or is he a selfish Magnificent Bastard who only cares about his goals of finding his father, becoming a Magister Magi and saving Mundus Magicus and making sure that his students don't get hurt is just a way to make sure he doesn't fail his training and is apathetic to anything that doesn't involve those three things.
Anti-Climax Boss: The True Final Boss of the series. After coming back and oneshotting Negi and Fate, the Lifemaker does absolutely nothing to prevent the girls from freeing Asuna, holding the Villain Ball until he's oneshotted himself by Negi and Asuna in a single chapter's span. Then he's defeated one final time off panelduring a Time Skip.
Most new pactio formed has a good chance of being exactly what the gang needs at that very instant, but most of them are predicted due to the girl's personality, a fact that's taken advantage of on several occasions.
The fandom does not appear to mind Jack Rakan's self-aggrandizing statements about his power and abilities (To quote him, "I have no weaknesses!") - probably because he more or less lives up to his claims, and then some.
The Anime Final movie also seems to be causing this, for similar yet different reasons.
Base-Breaking Character: Negi. Some consider him a dull protagonist with little Character Development, mostly due to having probably one of the worst cases of Aesop Amnesia in shonen history. Others find him genuinely compelling in his goals with an intriguing backstory and character dynamic, especially in comparison to other protagonists in the Harem or Shonen genres (who can often be quite dull compared to their co-stars).
Creepy Cute: Chachazero often falls into this, since her psychotic tendencies are entirely played for laughs. And she has miniature sized wine bottles that she drinks with Chamo − whether she can actually drink is anyone's guess.
Damsel Scrappy: Ako somewhat comes off as one during the first half of the Mundus Magicus arc. The initial problem involves Ako getting herself, Akira, and Natsumi sold into slavery, resulting in Negi's mission to find the rest of his students to take a back seat somewhat due to him and Kotarou having to take part in a tournament in order to get the money to buy their freedom. However, most of the main ire comes when Negi receives an artifact that allows Negi to use the artifacts of his Ministra Magi, and rather than using this as an opportunity to allow her to make her Pactio, Ako instead just wishes good luck in the final match against Rakan, resulting in the whole "slavery/tournament" sub-plot (outside of Negi meeting Rakan and training with him) being almost pointless.
"Magical Happiness", "Re-Born", "Maze of the Dark".
"Get a Chance!", "Good Vibration", "Magical Twinkle Sky"...Basically every song they've made could qualify.
Ending Aversion: The ending of the manga is considered quite unsatisfactory, to say the least. The main plot with Negi's father is resolved off-panel, a bunch of unanswered questions are left behind, and in general, lots of plot points are brought up right at the end and then quickly set aside.
As part of Negi's and Kotaro's training in a diorama for their match against their mentor Jack Rakan, they do press-ups with huge rocks engraved "Defeat Rakan-san" on their backs. Later, they return to the diorama after Fate defeated and erased Rakan from existence to discuss strategy; the rock is still there.
During Tsukuyomi's first appearance, she mentioned wanting to make Setsuna and Konoka hers. That comes off a lot differently now given... what we know now.
Memetic Molester: Tsukuyomi's In Love with Your Carnage tendencies have made her this, which is pretty much in character. Ayaka too her incredibly creepy attitude whenever Negi is around can make her a borderline child molester and get her arrested in some countries.
Moe: The series in general, especially in regards to the female characters.
Fate pretty much flies over it when he tries to KILL Negi with a stone spear through the back.
And Tsukuyomi does the same thing when she tries to rape Setsuna.
Narm Charm: The official English translation of the Manga, specifically Ku Fei's semi-Hulk Speak dialect. It's a spotty means of translating her tendency to stick '-aru' where it shouldn't be, but it grows on you after a while.
We're never gonna let Nodoka forget her "desired solution", are we?
No one is ever, ever going to forget Chachamaru's winding incident. Probably 'cause they just keep happening.
There's also Chachamaru getting chopped in half. It's become a sort of mini Meme in certain parts of the net to photoshop various reasons for her to be cut in half, like a Rider Kickfor instance◊. It was even animated in Final. Cue videos and animated Gifs to the same effect popping up.
Anya is markedly less popular than most of the other characters. The two main reasons for this are her Bratty Half-Pint / Tsundere behavior (made worse by the fact that she appears extremely immature and petty compared to the rest of the cast), and because she has very little actual plot importance, making her presence seem kind of pointless. It doesn't help that you'd think Negi's childhood friend would play a big part in things or at the very least shake things up a good deal by appearing, but she ultimately didn't amount to much and was soon lost in the tidal wave of characters.
Fate also isn't liked by the fanbase because of both his emotionless personality and the fact that he had tried to kill Negi with a stone spear through the back. Even after all of the crap that Fate had put Negi and the others through in the Magic World, he doesn't suffer any karmic backlash for his actions in the end and that Negi eventually befriends him, making Fate a Karma Houdini to some fans who found his Heel–Face Turn unbelievable and unsatisfying. Adding more fuel to this is when he becomes a substitute teacher for 3-A while Negi works on his plan to save the Magic World, with him basically becoming a male version of Kanako Urashima to some readers.
Squick: To some people, the fact that alot of 15 year old girls fall in love with or even are merely attracted to a 10 year old is Squicky. Especially with Ayaka her Freudian Excuse doesn't do much to lower the squick.
They Wasted a Perfectly Good Plot: Chapter 352: Asuna is now 130 years in the future on her own, though sad because of the fact that she has lost everyone she loves. It almost seemed like the premise for a new series centering on Asuna in a new world and becoming the heroine of her own story. But no, instead Akamatsu decided to take the Writer Cop Out, by having Chao conveniently appear with not only the Time Machine, but the gigantic Ass Pull that is the Inter-dimensional travel machine, and have Asuna go back to the exact moment that she left, making her supposed sacrifice redundant.
Too Cool to Live: In chapter 278, Rakan finally succumbs to the might of the Code of the Lifemaker and disappears in front of Negi. Then he comes back from the grave (briefly) to Bright Slap Negi out of his Unstoppable Rage. It just takes spirit.
Villain Decay: Notably subverted and twisted with Evangeline: although after her first defeat, she is no longer really an enemy, she later reveals (several times) that she is far, far, far more powerful than she let on at first, making her absolutely terrifying. Among other things, she uses her ice magic to shatter a demon several hundred meters tall, she KOs an extremely skilled martial artist in one hit without her magic while she was distracted by thoughts of Negi's father, and draws a character into an alternate dimension (well, an illusion of it anyways) and proceeds to nuke said character multiple times. Motive Decay? Maybe. Villain Decay? Not even a little bit.
Being a happy little boy with an Unwanted Harem of hot cuties aside, Negi has been through enough pain, horror, and trauma in his short life to give the most hardened Child Welfare officer nightmares for months.
Chapters 352-53 Asuna is now stuck alone in the future with everyone dead, so what does Akamatsu do? Have Chao and Eva appear out of nowhere to take Asuna back to the exact moment she left.
Might be also the reason why both Negi and Setsuna suffer from so much Aesop Amnesia, because once it seems that they have finally overcome their issues and insecurities a few chapters later, they're exactly the same as they were before. It's possible that Akamatsu had no idea how to have these two characters develop after overcoming their insecurities and so had these two forget everything they had learned just so that they could learn all over again, because otherwise he'd have no idea what to do with them.