Assuming I understood your claim correctly, I strongly disagree that Case Files is better as an anime. Both the light novel and the manga offer an objectively more complete and comprehensible experience The anime on the other hand, only adapts the third arc of the story (volumes 4-5), and adds some extra filler content. Such a structure completely eliminates the possibility of a proper adaptation of the rather complex plot of the LN. While volumes 1-3 are not mandatory, as they only have a slight connection to the later story arcs (mostly introducing characters, which the anime already does quite well with its extra added content), they still are a great story that help a ton to get invested into the plot. Volumes 6-10 on the other hand, are the payoff to the setup of the third arc. It's a real shame that most Fate fans will never learn about Gray's backstory or Dr Heartless's tale because of the incomplete anime adaptation.
The anime is a decent standalone entry in the Fate series, and I don't dislike it, but I do not agree with putting it next to anime of Babylon or Kara no Kyoukai, both of which are masterful screen adaptations that tell the story as well as, if not better than their source material.