In Season 2 of the anime, Mikoto's side of the Sisters arc takes 15 episodes (episode 2 to episode 16). While it is widely agreed to be better than the Index version of the same arc in nearly every way, the fact remains that the majority of the audience already knew exactly what was coming, so it was a bit frustrating it was dragged out so long.
Season 3 covers Mikoto's side of the Daihasei Festival arc in 15 episodes (episodes 1 to 15) just like the previous example, but was dragged out in a different way, mainly due to delays caused by the Coronavirus Disease 2019 Pandemic, causing its conclusion in late May.
Thanks to the Railgun anime, Saten Ruiko has become one of these. Her fans find her a refreshing character among the Four-Girl Ensemble due to being an Audience Surrogate with no powers, to the point where she was popular enough to make it to the Top 8 during Saimoe 2010. Her detractors call her a blatant case of This Looks Like a Job for Aquaman, being put in plot-relevant situations to look good at the expense of the competence of the other main characters no matter how little sense it makes.
Haru'ue is not the most popular character, but she's pretty well-liked in the community. While she's not quite hated, she has a bigger role in the second half of the first season than most people would prefer, largely because she was basically created just as a device to connect Kiyama's children back to the plot.
Touma from the main Index anime is disliked by some fans loyal to the Railgun series, being a Spotlight-Stealing Squad in the first half of Season 2 who hijacks Mikoto's plot in the Sisters arc. The fact that he fights and defeats Accelerator, with Mikoto acting like a Damsel in Distress who can't do anything without him, really doesn't help. Of course, this can't be helped in the slightest since the Sisters arc was originally Touma's story in Index, giving more details on Mikoto and the Dark Side of Academy City. The Railgun version was written as a Perspective Flip; we know from the start she isn't the one who's going to solve the plot.
Misaki Shokuhou was hated by the fanbase for her very manipulative personality, especially in her appearances in Season 2 and the first half of Daihasei Festival Arc in Season 3. One particular scene that made the fandom mad at Misaki was when she erased her memories of her friends, which is later revealed to be her measure so that Mikoto's friends will not intervene in her plans to take down Gensei. Manga and light novel readers also reacted this way, but their hate for Misaki subsided as much earlier than anime-only viewers, as the manga and light novel revealed her true intentions, as well as her connections with Dolly, in the latter half of the arc much earlier.
The anime original arc that ended Season 2 has caused a lot of division among fans. Many find the camp and Power of Friendship levels over the top, are angered at how Misaka is given the Idiot Ball a couple of times, and express frustration at the many plot holes in the arc. Others absolutely love the arc since it addresses the primary problems of the Sisters arc (notably Misaka not going in alone) and everyone gets a chance to shine against STUDY.
In general, the filler JC Staff made for the series is very polarizing. While one group of fans likes it because it gives screentime to the other characters not named Mikoto and enjoys the Slice of Life scenes of those episodes, other fans find them annoying, pointless, and boring. It doesn't help that some of them come after the Sisters arc, which is considered by the majority of fans to be the best arc of Railgun and one of the best of the entire Raildex universe. Luckily for that camp, Season 3 does not have filler arcs anymore.
Kihara Gensei, the patriarch of the Kihara family, is responsible for nasty experiments on children which resulted in many of them suffering permanent trauma, all so that he could create a powerful Level 6 Esper. Gensei has no compunction about murdering people in his path. The first "sample" of his experiments was his own granddaughter: Gensei overloaded her mind to collect samples from her, and repeated this process on other children as well. Gensei is fond of manipulating his own family members into becoming his test subjects, even though he knows that a massive surge would possibly destroy all of Academy City.
Gensei's granddaughterTherestina Lifeline is just as cruel and twisted. Wanting to follow Gensei's example, Therestina abducts children and puts them in comas so she can harvest the samples from their minds. Gensei manipulates the young heroines into providing cover for her, all the while intending to overload the minds of the children she keeps under sedation, fully aware this will destroy all of Academy City and not caring as long as she achieves the "perfection" she hungers for.
Fanon Discontinuity: The second story arcs of both Railgun seasons usually get this reaction from fans for being anime-original arcs, the Febri arc from Railgun S even more so.
Foe Yay Shipping: Misaka Mikoto vs. Misaki Shokuhou, which leads to the cute portmanteau MisaMisa.
"Funny Aneurysm" Moment: Chapter 47 of the manga, adapted to episode 3 of Railgun T, features the first time in the franchise that Touma is seen interacting with Misaki Shokuhou. Aside from the fact that Misaki somehow already knew Touma's name, the meeting is played up in a humorous manner, with Misaki acting silly and Mikoto casually being mocked. However, around two and a half years after this chapter released, Volume 11 of New Testament: A Certain Magical Index, came out, revealing Misaki's backstory with Touma, including how tragically Touma can't retain memories of her due to brain damage. This puts that meeting in Railgun in a new light: Misaki suddenly re-encountering the boy she has feelings for, a boy that she knows will never retain memories of her. And not only that, she is with her rival, who also has been regularly interacting with that same boy as of late. It's not a surprise that after episode 3 of Railgun T aired, sales of New Testament Volume 11 shot up.
Harsher in Hindsight: The MISAKA Network dorkiness, especially considering that many of them are gonna get brutally killed off.
For Gensei Kihara, having ten kids forcefully overloaded with esper powers definitely crosses the line. And before that, using his own granddaughters as the subject of his experiments. One was involved with the Level 6 overload experiments, the other became a cyborg. And then there's what he does in Chapter 61 (episode 10 in Railgun T).
Therestina Lifeline Kihara planning to overload the child Errors that her grandfather created so she can become God and destroy the entirety of Academy City to boot. On top of maliciously manipulating the cast, practically turning Uiharu and Kuroko against each other, and her brutal beatdown of Misaka after using her Kryptonite Factor on her.
More Popular Spin-Off: While Index was a hit, Railgun was more popular, sold more DVDs and got a better reception with fans thanks to a lot of Character Development for the cast. This is probably because it's also partially a Schoolgirl Series. Furthermore, in a world where crazy people wields crazy superpowers that get thrown around with reckless abandon, the main characters of Railgun seem like relatable humans (see the case with Saten, above). Note however that this is only true of the Index anime. The Index novels sell hundreds of thousands of copies and are the most popular medium of the entire verse by a healthy margin.
Padding: The anime increases the importance of Saten and Uiharu, adds a fifth girl from a filler arc, and then has the three of them, Kuroko, and Mikoto frequently wandering around making small talk and eating things. Not much of this is really relevant to the ongoing plot arc, so when an arc gets into full swing, the three less important girls tend to get brushed aside so that the original mood of the story can remain intact.
The Scrappy: Because of her actions at the time, Uiharu was absolutely loathed by the fanbase throughout most of the final episodes of the first Railgun anime season, namely her constant Wangst and denial of Haru'ue being the cause of the Poltergeist occurrences, despite the fact that the evidence can be seen with a naked eye. It was only when Kuroko gave her a much-needed slap in the face that people started warming up to her again. It also helps that this took place in anime-original content, giving Uiharu a free pass despite her actions.
It's very hard to not feel sorry for Mikoto in the Sisters arc. It is already hinted in the Index version of the arc, but we only find out about how much trouble and suffering she goes through when the Railgun version comes. From finding out about the truth of the inhuman Level 6 shift project she agreed to help with as a child (it doesn't help that it was disguised as a cure for muscular dystrophy a very well-meaning intention), witnessing clones of hers being brutally murdered, her attempts of desperately trying to stop the project (which involve her sacrificing sleep and food, as well as risking herself getting beaten down by the ITEM squad), and finding out that her efforts did little and just barely slowed down the project, to her finally breaking down from all the guilt and despair she suffers, and even contemplating suicide for it if it wasn't for Touma stopping her. At this point, you'll just want to give the poor girl a hug and tell her that everything is going to be okay.
The Sisters count too, considering how they were created just to be brutally murdered by Accelerator in the Level 6 Shift project. This is especially apparent in the flashback of the first clone's death, where she mumbles something along the lines of "Is this death...?" and "Cold..." as she is slowly dying. 9982 probably gets the worst of them all, what with her leg getting ripped off (doesn't help that she is visibly pained during that moment, which is especially jarring considering she showed little emotion up until this point) and her smiling while holding the Gekota pin Mikoto gave her beforehand before getting crushed by a train locomotive.