It seems odd that the Touma vs. Accelerator fight was called the Weakest Vs. the Strongest. Sure, Touma may be a level 0, but there are others, and he's not exactly physically weak either. But Touma, due to his power doesn't come up under the scans at all, while even other level 0's do (we saw Saten had been given grades, despite being a level 0). Since he shows no power in either the scans or tests, officially, he really is the weakest ESPer. From chapter 5 of A Certain Scientific Railgun manga:
His right hand contains a mysterious power that he calls the "Imagine Breaker," but Academy City's system scan is unable to detect it, so officially he is a Level Zero.
The Sisters' method of self-narration initially initially seems like just an oddball quirk that they share. Something to distinguish them from other characters in the series. But watch Episode 17: Misaka-10032 made the following comment to Last Order: "If you have said that, then it has already been broadcast through the Network. So there isn't a need to say that again in words." Their self-narration isn't just a quirk, it's how they input information into the Misaka network so all the other Misaka know exactly what's going on. This theory seems to be enforced by Misaka WORST, a Sister who isn't directly connected to the Misaka Network. She's still a Third-Person Person, but doesn't narrate herself because she has no one to narrate to.
Touma is the only known person with the ability to cancel out anything out of the ordinary, and due to how he fights his opponents, Touma represents the true nature of humans. Think about it, he figures out normal ways on how to deal with supernatural opponents, is firmly grounded on reality, and relies on his own skills rather than on his abilities, and if you kick his ass he will just get back up.
Much like their speech style mentioned above, it seems odd that the Sisters all wore the Tokiwadai uniform as opposed to "civvies." But it's a rule at Tokiwadai, as stated in Railgun that students must wear uniforms at all times. The Sisters are wandering around town, and Mikoto is well known. The reason they all wear the uniform is so that they don't inadvertently get the original Mikoto in trouble at school for breaking the rule. This is also why Last Order and Misaka Worst don't wear it. They're too young and too old looking respectively to be mistaken for the original, so they can dress however they want.
The Sisters arc seems like it has a large number of plotholes, with explanations that occasionally contradict earlier information. That's because the experiment was fake the whole time. Aliester needed a reason to create all the Misaka clones for his Artificial Heaven, so he made the Tree Diagram tell all of the scientists that they needed to make them in order to turn Accelerator into a level six. If any scientist thought it was ridiculous they would of course just assume that the super computer was right and they were wrong, so it was the perfect cover.
Know how the Right Seat of God managed to mostly purge themselves of the original sin? The original sin would be Adam and Eve disobeying God. And how did they disobey God? By eating the fruit of the Tree of the Knowledge of Good and Evil. Therefore, the Right Seat of God are people that mostly do not understand Good and Evil, except for Acqua who is a natural born Saint, which may be why he is the only one of them that wasn't a complete bastard to begin with.
Accelerator's Black and White Morality. He pretty much grew up in a lab and has little "real" experience dealing with normal, sane people. It falls in well with the naive and childish part of his psyche. He never could see the grey in things.
It's been stated that Touma terrifies the Kiharas. This makes sense when you realize that the Kiharas are amoral scientist who rely on analyzing their enemies to defeat them. Touma however, has an unexplainable divine power and a mindset that makes no sense to the Kiharas. He is the one person they can not analyze, and thus he terrifies them.
Why does WORST fire nails instead of coins? Well, basic physics. The equation for kinetic energy is (1/2)*mass*(velocity^2). Since WORST fires at Mach 1 instead of Mach 3, she effectively fires at 1/9th the kinetic energy Mikoto does when using an object of the same mass. If she can fire an object nine times the mass of Mikoto's coins, she achieves the same kinetic energy. Since nails tend to have more mass, she compensates for the lack of speed that way. It's the same effect that's shown when Mikoto railguns objects larger than her coins.
Episode 18 in the second season has Touma running into Misaka Imouto. When he buys her some animal-shaped pastries, she thinks the chick-shaped pastries are actually real birds and is horrified when Touma actually eats one. This seems silly at first and looks like something that Touma could easily handle by setting Imouto straight...until you realize that in order to explain the situation, Touma would have to use some of the very same rationalizations that were used to justify the Sisters being mercilessly slaughtered in the Level 6 Shift experiments in the first place!
Pretty much everything about Academy City becomes much darker when you look at it closely. Especially after learning about the parameter list. For instance in Academy City there are a lot of orphans called "child-errors" whose parents took advantage of Academy City's boarding school nature to abandon the kids there knowing the city would have to take care of them. This doesn't make much sense when you consider that the city surely has enough resources to preform background checks on the parents, which would save them money in the long run from not having to look after abandoned children. But then of course you realize that Academy City lets in the children because there is less of a hassle if you perform painful and life threatening experiments on children who don't have parents to raise a fuss.
Academy City isn't a city of science and technology, it's a gilded cage for the army of level fives they're attempting to produce in order to make the world their plaything, led by a regime so cruel as to make the Warhammer 40,000 universe look like the home of Amnesty International. Logic on this is supported by several things:
The cover-up of the Parameter List and the implication that they knew Misaka Mikoto would be a level 5.
The willingness to lock up Takitsubo Rikuo due to her "academy individual" potential, as well as the fact that they entered World War IIIspecifically to unlock it, all so that they could create an army of level 5's and cull what the helmeted board director called "unnecessary abilities" (i.e, anything not related to militarization).
If Academy City was only interested in research potential, then they would share their technology with other nations to increase the amount of lines along which tech is developed (like how the US shares all the non-military tech it develops). The fact that it doesn't shows purely malicious intentions. For example, Yomikawa Aiho claims that people outside, even the best and the brightest from MIT can't understand Academy City's best tech, and that's the reason they're not releasing it, which is complete and utter bullshit. The reason science exists is because it can be understood given time and research, by anyone. Did anyone other than Thomas Edison understand the lightbulb when he developed it? No, but he demonstrated the technology and taught others how to replicate it. Same with Alexander Graham Bell and the telephone.
The willingness of Academy city to assassinate the families of espers who left the city, as well as the creation of special forces teams such as GROUP, ITEM and SCHOOL to suppress any and all dissent amongst the populace, using force as the first and only option. Also, their assassination of the US senator who tries to restart the Stargate Program (which it seems that Academy City originally sabotaged in the first place). Also, Academy city seems to be in possession of a massive brain-trust, as though every single MIT grad simply went there, or anyone with an IQ of 120+, which is unusual because it would be political suicide to concentrate every single R&D program in one nation with dubious ties.
The Daihasei; it's a sports festival, practiced along the lines of fair sportsmanship, but this is averted; espers are encouraged to use combat grade powers against the opposing team, to the point that all Tokiwadai has to do is simply knock unconscious every single person on the team opposing them. This is malicious for two reasons:
It encourages the idea that it's ok to use lethal abilities on regular people.
It can be said that Academy City also serves as a way to control the members of the Kihara family. Without Academy City, the tech it has would be released into the world and Kiharas would start popping up all over the place.
Granted, you can't easily dissuade a person committed to action. But nobody, not even people who you'd expect to know their way around the Bible, ever even begins to attempt appeals to Scripture. Anywhere. Even where it would make sense, as with the nun-vs.- priest showdown. The best that you get is some vaguely Catholic-sounding pronouncements. Sure, if someone pointed out the Church was violating Thou Shalt Not Kill the answer would probably have been "You're heathens, you don't count," but it would have been nice for it to brought up.
There's no way the Vatican would give so important responsibilities to women.
And there's no way the Vatican would ever support a group like "God's Right Seat", even before maniacs like Vento and Fiamma came into it. Their entire purpose and the powers they possess are anathema to very central Church teachings.