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.
Accelerator: A young man who's trying to redeem himself for the terrible things he has done while trying to avoid turning back to his past self or a sadistic heartless monster who hasn't changed his ways and enjoys being a powerful killer.
Contemptible Cover: The cover of New Testament 9, widely considered one of the best volumes in the series, has nothing but a picture of Othinus wearing the equivalent of Chainmail Bikini.
Critical Research Failure: The reason why Stiyl looks so old despite supposedly only 14 was because of a miscommunication between the artist and author: Touma and Stiyl's first confrontation was supposed be something of an Old vs New (which the artist took literally to mean "old man vs. young boy"), completely missing the note that said Stiyl was only 14.
Now with the second season of Index, Fukiyose Seiri has become very popular with fans on her debut in Episode 8.
Fanon: Fans have speculated that the Amakusa Catholic girl that Touma fought and saved from a fall in Volume 7 may be Itsuwa, the Amakusa warrior who was first introduced in Volume 11 which may explain why she has a crush on Touma in the first place. However, the 2nd season anime had it Jossed as it wasn't Itsuwa that Touma saved but another girl.
It's also fairly common fanon that Laura Stuart is Index's mother, especially since the two are specifically drawn to resemble each other. This also adds an extra Kick the Dog element to Laura's treatment of Index if you buy that theory.
Fans have theorized for years that Aogami Pierce is the sixth level five, by this point they would be furious if it turned out it wasn't him.
Fan-Preferred Couple: Majority of the fans ship Touma with Misaka. Though after NT 9, it seems to have shifted to Touma with Othinus.
"Funny Aneurysm" Moment: Index-tan Episode 2: Himegami is asked what her wish for the second season is. Her response? "Um, I won't ask for my episode, but I just want to be treated more-". Guess what happens in her first lengthy appearance in Season 2? She gets filleted by Oriana Thomson because she thought that Himegami was an agent of Necessarius due to the Celtic cross around her neck.
God-Mode Sue: Accelerator. He can modify and redirect vector values of anything by touch, bend the laws of physics to his will, understand unknown or strange laws hitherto unknown to him and making use of it, can survive a nuclear missile, its shockwave, heat and radiation, and it's subconscious, meaning that it is active all the time. The only things that can counter it are the Imagine Breaker and attacks that are built upon laws or vectors unknown to him.
This is only partially true: As of the second to last arc of Season 2, we know that even non-espers can damage Accelerator, as long as they utilize special properties of how his power was trained/developed in the first place (as seen through Kihara Amata). Not to mention that Accelerator experiences "circumstances" that make him lose his powers, and the only way he can use a weakened version of them after this incident is through outside assistance.
Harsher in Hindsight: Academy City's Power Curriculum Program. In theory anyone undergoing this program can become an esper yet there are still people who have yet to gain powers and even those who did never go a higher level which suggest the program has some problems. However Vol. 22 reveals the program is secretly being undermined by the Higher Ups of Academy City who decide who can and cannot gain esper powers and/or go a higher level based on the type of the powers that person has. This revelation makes it much worse once you realize Level 0's like Saten, the Skill Outs gangs and low level espers like the Level Upper users, who work hard to gain powers/higher levels but never can because their training is being sabotaged as the Higher Ups see no point of helping anyone who doesn't have the powers they want. That's right, the city is responsible of destroying the dreams of many students and leading them into path of cynicism and crime!
All intentional; while Mikoto claims in SS: Liberal Arts City that Academy City has no intentions of taking the world via military force, the revelation via Chapter 22 suggests otherwise. Why else would you try to make an army of level 5s or an "interceptor" aircraft that has the ability to fly halfway around the world and level a city single-handedly? Basically, the reason why the corporate crooks of AC haven't bothered leveling the level zeros of their population isn't just because they don't want to, its because they need cannon fodder; they needed a group of disgruntled individuals who they knew would resort to violence in order to defend themselves against those termed and rewarded for being genetically superior, so that they might label that group as people on whom it is okay to use your powers, people whom it is okay to murder, because no one will care about them due to their collective reputation.
Holy Shit Quotient: A large portion of the series, but the entirety of Volume 22 and New Testament Volume 9 are probably the biggest. Especially NT Volume 9.
Every new book (except arc finales like Volume 22) usually makes the Holy Shit Quotient go way higher than the previous book. NT Volume 10 takes this to an extreme arguably outdoing even NT volume 9 with its insanity especially in its epilogue.
Iron Woobie: Touma gets his ass kicked on a regular basis, and even the fights he wins tend to end with him in the hospital. There's no real explanation for why he puts himself through such misery, especially considering he has his own inherent bad luck to deal with. And yet he claims to be happy with way he lived his life...
But he always does win in the end, and women fall like flies to his two-dimensional Shonen Protagonist hero speeches. What's not to be happy about?
The novels explain all of this in detail... eventually. Volume 22 summarizes it quite nicely, though NT volume 9 best outlines his "real motivations." NT volume 9 partially trolls and explains that Touma doesn't really believe half of the "hero speeches" that he gives to villains. He just does this to briefly get through to people who have temporarily gone crazy as a result of experiencing severe loss/tragedy in their lives. As of NT volume 9, he has a higher moral ground and it is actually justified because of what he went through...
Jerk Sue: Misaka is smug, rude, violent, and a generally unpleasant person... and is loved by practically every character, and got her own spinoff.
New Light, particularly Bayloupe and Lessar, though Floris and Lancis aren't exactly innocent either. The group seems the be well aware of their apparently abnormal closeness too.
Floris: "Hey, you two lesbians who look like you’re from some erotic novel or something." note Said when Bayloupe and Lessar were in a compromising position in the back seat of a car.
Lessar: "Floris! Lancis!! Quit awakening strange new tendencies and wake up! We need to use this room!!" note Said when Lessar found the two sleeping in the same bed when she needed to have a chat with Mikoto. Apparently Floris just likes to crawl into other peoples beds when sleepy.
Special mention goes to Komoe-sensei, which is even in her name. She's also not above invoking this trope in order to guilt her students into doing things.
Quite a few of the Sisters, but 19090 stands out. She's a minor side character, but in her first appearance (when the four Sisters still in Academy City were getting sized for their winter uniforms), the others discovered that she wasn't quite as identical as she was supposed to be, due to reading girly magazines and dieting. She runs away tearfully, while her Sisters hunt her down ruthlessly in an attempt to measure her more precisely and force her to fix her eating habits.
The researchers involved in both events under the For Science! entry above cross this line in a big way. Accelerator also crossed the line before he's even seen; however, he seems to be trying to come back from it. If you can forgive him...
Narm: Apparently, Accelerator can state-change air into plasma by making ridiculous noises with his mouth, though the ridiculous noises are another form of his evil laugh. This is also a case of Formulaic Magic, those noises he was making were Accelerator performing the calculations necessary to use his Vector powers at high speeds.
Never Live It Down: No matter how much good he does or how many heroic acts he does, some fans still hate and can never forgive Accelerator for the terrible things that he's done especially what he did to the Sister Clones before his Heel-Face Turn.
Ship-to-Ship Combat: Which girl should be with Touma? Don't ask! because the moment you say so, you will get yourself in a nasty Ship-to-Ship Combat between other fans over their favorite girl!
Yet two of the biggest Ship-to-Ship Combat by Japanese fans are the Mikoto x Touma fans and Kaori x Touma fans. These two fanbases are so big, the novel artist Kiyotaka Haimura knows it and even drew about it!◊