I'm still watching it and still enjoying it. There are a couple of weak story arcs in the middle, but I'm a fan of the breather episodes and the season's last big story arc gives us pretty much open war.
This season's slight problem, for me, is that I prefer its science episodes. "When science and magic cross, the story begins," is said at the end of every episode. That's usually false. Academy City is all about science and psychic powers, while the world's Christian churches are all about magic (and assassinations, evil and world domination). Yeah, I know. Go with it. Personally I don't think it's offensive, because it's all just light novel ridiculousness and it would make as much sense to get upset about historical accuracy in anime that have 16th century samurai piloting 30-foot-tall battle robots. However I also don't think the show's various churches are inherently that interesting. They do bad things. They squabble among each other. I don't really care much.
The Daihasei Festival arc (eps.8-13) drags on a bit, while the Queen of the Adriatic Sea arc (eps.14-16) is saved by the casting of Norio Wakamoto. Ep.16 would have been dull if Wakamoto's mighty overacting hadn't been making me laugh. Even the magical characters tend to be less interesting than the scientific ones, for me, although that's mostly because the scientific ones live in Academy City and go to school with Touma and have better defined relationships with each other, whereas the magicians are outsiders. (The exception to that pattern is Index, who's theoretically cute and lovable, but I don't like her bitey tendencies. Human bites are nasty, usually worse than animal bites because our mouths contain more bacteria, and a bitey child is one of the worst things you can have in a primary school class.)
Anyway, for what it's worth, Christianity in this universe includes the Roman Catholic Church (super-evil), the Church of England (moderately evil but can be a useful ally against the Catholics) and the Amakusa-Style Remix of Church (Japanese sect that's presumably the successor of the real-life Edo-era churches that had to stay in hiding to survive). The Russian Orthodox Church is only mentioned in passing, as an ally of Rome, and so far the Anglicans have been the only significant protestants. Don't think about the meaning of the word "Saint". Also the Anglican Church has a black ops division called Necessarius (aka. the Church of Necessary Evil), while Rome has a paramilitary organisation called Agnese Forces. These are all sexy young nuns, sometimes wearing what I can only call mini-habits, but it has to be said that religious gender equality has flipped in this universe. Most characters are female, whatever the context.
There's still plenty to enjoy even in those religious arcs. They're not a write-off. The Daihasei Festival arc conclusion includes a villain vs. villain that made me laugh, since Rome vs. Anglicans has historical basis and it's funny to see the anime go this nuts with it.
The established characters (especially the RAILGUN cast) don't get as much screen time as I'd like, but they're a laugh. The Misaka sisters are surprisingly funny, despite theoretically being personality-free clones, while Accelerator is cool (in a psychotic way). He's probably the season's most interesting character. The Tree Diagram Remnant arc is like a RAILGUN crossover, while the small-scale, funny early episodes of the Academy City Invasion arc were my favourite of the season. (The city then turns into a warzone.)
It's still a deceptively violent show. For such an apparently light series, the fights can get nasty and the slightly bewildering web of secret organisations don't care about human life at all. "Good job. We'll transport the bodies and eliminate the evidence." The season's most startling moment might be the Agnese Forces' counter-move against Index's magical ability, Sheol Fear. It's both gross and thematically interesting as a response to the Church having flaws exposed in its doctrine.
Minor niggle: no one ever thinks up counter-measures for Touma's anti-magic ability, even though he keeps foiling the baddies' plans and there are lots of juicy options. Levitate a twenty-ton stone slab inside a room, for instance, then hide it with a flimsy fake ceiling. If Touma uses his Imagine Breaker power, splat. That said, though, villains are quite likely to come up with logical, ingenious ways to beat, say, Misaka, Kuroko and especially Accelerator's powers.
The show's still fun. I'm ploughing through it at a rate of knots, which proves if nothing else that it's marathonable. It's pretty mental and increasingly ambitious with the complexity of its political factions and the global scale of its stories. It's still silly light novel fare, of course, with Touma having entered a room with a naked girl in it so often that he's developing a fear of walking through doors. (Seeing a girl naked means a physical attack, obviously.) Next up: A Certain Scientific Railgun S.