I am not sure that I prefer the anime or the manga better. Each has their own respective charms that I find endearing. To say that I enjoyed the illustrations of the manga should not downplay the enjoyment I gained from hearing the seiyuu in the animation. I do not think their differences are comparable being two different forms of media.
I liked the little added scenes here and there. The only changes I did not enjoy were overlooking the cameos of characters primarily from Index, such as the single panel with Oriana Thompson, or the gag with Fukiyose and Misaki. I can understand why the Fukiyose scene was changed.