The story. What can I say? I just didn't really like them. Most of it has to do with the characters, which I will elaborate later on. The story arcs didn't lead to anything big in the end. There was no big climax or anything; they just left an ambiguous ending, sequelbating. The arcs seemed to be half religion half science. I would be okay with that if the two were actually mixed together but they were kept apart. It was more like it was half Index and half Railgun. At the end of each episode, they say that when magic and science cross, the story begins. That's the problem; they never crossed. Characters from their respective shows didn't really mix with the other either, and that was kind of disappointing. One of my biggest qualms with this show is how each arc ended. Some of the most unoriginal endings ever written. I can break it down. 1. Touma is the last man standing 2. He gives some terrible speech about care and love and other unimportant stuff and 3. He punches a woman in the face. How anti-climactic is that? You'd expect an epic ending with something magic or science related used against the enemy, but all you get is a punch in the face.
The characters. They have changed so much, and not in a good way. Touma seems even more self-righteous than usual. Index seems even more useless than usual too. She was very annoying, one of the most annoying characters in the series. You know, I didn't laugh the first time she bit Touma on the head, so why would I find the 46th time funny? Why are all the characters pandering to the fans? Who thought this was a good idea. I don't want to see every single female character wanting Touma little head (except for Index who wants his bigger one on his shoulders). They turned so many of them into tsunderes when they clearly weren't that in the previous season. Why? One is enough (well, one is too much, actually). Mixed in with these terrible story arcs, I've grown to hate these characters that I used to like. Oh, and there's fanservice. Some of the stupidest fanservice I have ever seen. In many shows, you have the panty shot, which is understandable because the camera just happened to be at an angle to see it, but it index, the characters strip down for you! Terrible.
The art is very generic. The animation is average, I guess. Pretty much the same as the first season and Railgun, so I don't really have complaints about it. The music was really boring. It's some very generic music. I didn't really like the OPs and EDs either, but the first OP was alright. There seems to have been very poor artistic direction. Any art is just drained to almost nothing, and art is something that I crave. Oh well.
Overall, I pulled nearly no enjoyment from this show at all. I absolutely hated the characters and story arcs. Very little logic was used, like that grenade in one of the later episodes that exploded in a small room and did barely any damage to the room and not even injuring anyone in the room. Logic was not on the menu for this show. J.C. Staff took something I really enjoyed and turned it into this ugly, disfigured beast that I found nauseating. I really hope they stop there and stop ruining it further. I can't say I have high hopes for that.
Then again, I'm pessimistic.