Why was Rakan able to escape from being erased twice even before Cosmo Entelechia was undone? Poyo revealed that Cosmo Entelechia is a perfect version of the Lotus-Eater Machine she trapped Ala Alba in... but what the hell could you possibly give Jack Rakan to keep him there? He already quite literally has everything he could ever want. And he has already shown that he knows a way to escape from pocket dimensions.
Fate's name seemed to be merely chosen for it's coolness factor. Then a long ways down the road, his Reality Warper abilities are revealed, and while fighting Jack Rakan he points out that because of his power, the outcome of his fights are predetermined to end with his victory. Which certainly gives a new level of meaning to his name, they aren't just fighting an enemy named Fate, but literally fighting against fate: a predetermined outcome. This means Eva is so strong that destiny itself won't dare fighting her, for two reason: he knows she is too strong to defeat, and fears she'll bring Screw Destiny to the literal conclusion... Then here's another about his surname: Averruncus is the ancient Roman god of disaster aversion. Which makes sense, as that's exactly what he's trying to do in the Magic World, as far as he tells us. However, Averruncus is also known for causing just as much damage as he prevents, intentionally or otherwise. Thus, why Negi absolutely must stop Fate: even if Fate does theoretically save the Magic World, it's guaranteed to bite everyone in the ass somewhere down the line.
It seems like a standard shonen fight... until Rakan (and by extension the reader) realizes that Negi set up his Taiindou circle way back during his initial exchange of blows with Rakan (with Raiten Taisou 1); in other words, he had to use it all along (though it seems to be more of a plan B if Raiten Taisou proved insufficient).
On the same subject, Negi fought for quite a while with Rakan. It ended in a draw, but Rakan said it counts as winning and gave him the prize money anyway. Nagi's fights with Rakan always ended in draws, too. So, by the result of a draw, it means that Negi has reached the level of his father, and by this, Rakan knows that Negi has reached his goal in life, thus has achieved the prize.
Demon Negi's ouka houkens seem so much weaker in comparison to the normal Negi's because Demon Negi isn't even capable of coherent thought, why would he be capable of focusing enough to keep 100 or so magic arrows focused into a single direction?
Negi's wielding of a sword and the staff right before the trip to Wales seemed odd. But the sword represents his mother and the staff represents his father.
Ako just seems to be full of Fridge Brilliance. Her artifact's ability (essentially the ability to magically dope her allies) was kind of out of left field. But Natsumi's artifact, which reduces her presence, reflects her view of herself as a background character. So a large part of Ako's character is her belief that she's a "supporting/secondary character", right? What better artifact for someone who sees themselves as a supporting character than something that boosts the abilities of her allies instead of herself?
Where did the "ma" from Negima come from? Negi + majin (demon) = Negima. Akamatsu had it planned all along.
A minor one, but Chachamaru's non issue with Negi seeing her in the nude exists because to her SHE ISN'T NUDE. Remember she has a synthskin covering her body now whereas before she was exposed to the world, as it were.
Why is Cosmo Entelecheia always composed of an earth, a fire, a wind and a water user plus Dynamis? Because the Lifemaker was born 2600 years ago, when pre-Socratic philosophy speculated the world (Kosmos) was composed by each of the four elements, which move from potentiality (Dynamis) to actuality (Entelecheia) to form it. Pure genius on Akamatsu's part.
Negi and Fate's battle soon moves from the altar to the grounds below it. At first, that may just seem an attempt to not get the girls caught in the battle, but after Shirabe puts Asuna back in place, they actually can't fight there because of the anti-magic field she radiates. That is also why during their last attack, the platform the girls are standing on is outright shielded against it and why the mana vortex that managed to suck the Great Paru-sama in isn't powerful enough to completely blow the girls away.
Nagi's title of The Thousand Master. Theodora said in chapter 239 that one of Nagi's favorite high ancient incantations was... "The Thousand Bolts". Consider that Nagi probably had the magical capacity to use that spell over and over again, and we've got The Thousand (Bolts) Master.
Chachamaru's tears. How are the emotions are connected to laser?. But it can be quite simple. The distress she felt could be interpreted as danger by her programs, which could start preparing lasers just in case.
Remember Asuna's stated thing for older men, particularly Takamichi? Now, remember back when we learned Asuna is almost certiainly older than she looks... In fact, in that flashback, she looked about Takamichi's age... We now know that she is actually older then him that means she is really as big a Shotacon as Ayaka, just with the ages a bit mixed around
In chapter 352, Asuna wakes up after 113 years asleep protecting the Magical World to find that Everybody's Dead, Dave. Then, at the end of the chapter, Evangeline turns up with Chao, of all people, who they dimension-hop back to a few minutes after she left. Ass Pull, you say? It's actually pointing out that Negi, even with his vampire body, can and probably will die over the course of his life, and implies that Asuna being around can save him from whatever death might occur.
Evangeline's pactio card renders her middle name as "Ecaterina", indicating possible Russian ancestry. Albireo nicknames her "Katie". Now, the Russian equivalent of "Katie" is "Katyusha". As in, the awesomely destructivemultiple rocket launcher.
"I want to be friends with him" may sound a bit cheesy for something that helped Negi control Magia Erebea Encroachments, but when you read the few scattered thoughts of demon Negi, it's always about enemies he has to beat/kill/devour. Realising he does not have to be enemies with Fate - his main problem at that time, could really put his mind at ease.
The bulk of Negi's Inept Mage moments in the early chapters involved casting spells on Asuna... which means his skill and power were never an issue. At one point he offered to help Asuna with her paper route by flying her around on his staff. The reason this one is significant is twofold: The combined weight of Asuna, Negi, and the newspapers she was carrying really could have weighed the staff down and prevented flight (since we know Akamatsu knows his stuff when it comes to little details like this), and Asuna's antimagic nature would have prevented the staff from flying in the first place, which is something neither of them could have known at the time.
Evangeline was 10 when she turned into a vampire and stopped aging. Her vamp tendencies, which usually get played for laughs, get a lot more disturbing once you realize she never hit puberty. With all that she's seen in her five hundred years, she learned and knows about sex, but she probably never understood it.
Ako required a rare "cure-all" medicine to cure her sickness which cost a million Drachmas. Cue chapter 320, where it is revealed that Dryads are hunted down and their horns cut off and sold to create a "cure-all" medicine which cost a million Drachmas. Do the math.
From what they were saying, Slime Sisters could (maybe even did in the past) melt and eat humans.
Think about this: the existence of the timeline-hopper means those other timelines are still out there. Consequently, there's a timeline where Chao reveals the existence of magic, and Negi disappears with twelve schoolgirls. Some of whom presumably have parents and families who never find out what happens to them.