The main problems I have with the anime are that it failed to do its main character and its overall themes justice. Neither are portrayed in the same vein as they are in the novels. This isn't just due to just details but tone and choices in direction of the anime.
Plus, the anime paints the impression people have about the series and its characters moreso than the source material due to the fact that most people won't read the source material so it creates this annoying disconnect during discussion.
The anime was good in its own right. If it was not, I would not have ended up reading the novels in their entirety. However, it still fails as an adaptation to me. I understand that there is a lot of work that goes into animation but my point is still valid criticism.
Oh...I thought you had read the novels...
My bad...
Like I said, Railgun season 1 was littered with padding and had the Poltergeist Arc, which I can forgive somewhat in light of it being declared semi-canon and in light of the Silent Party Arc. However, the Silent Party arc spits upon the series and contradicts the canon.
This reddit comment explains a few of the problems with the Silent Party Arc.
Uuuu...do I have to pick? The magic and science sides of Index are both amazing. Hell, at this point in the novels we've reached a threshold where they can be indistinguishable.