As someone who watched this anime as a manga reader, my review will be reflective on that bias, just an FYI.
Personally, I thought this was a good anime adaptation. I liked a lot of the art direction and the score is absolutely to die for (I purchased the CD). I love the casting of the actors in both the Japanese and English dubs of the anime.

The first cour (1-12) were adapted from the manga very well! Some scenes were moved around to flow better. I don't have any serious negative thoughts about the first 12 episodes.

Moving onto the second cour (13-24) here is where I began to see some issues in terms of pacing and removing scenes. The Beast of Gévaudan was very rushed. The team made sure to hit vital points, but a lot of information was more in depth and detailed in the manga, while the anime glazed over certain terms and information--sometimes choosing to ignore all together.

In the midst of that, one extremely big omission from manga to anime is scenes with two specific characters. Loki (Luka's Brother) and Veronica (Domi and Louis's Half-Sister). I believe this was cut simply because they didn't see Loki or Veronica's scenes to be relevant to the overall timeline as they were trying to cover the arcs and stick to the 4 major characters. This is the most negative qualm I have about the anime adaptation.

MAJOR SPOILERS FOR EPISODE 24

Moving onto Misha and the amusement park arc. I honestly didn't think we'd get this arc covered in the anime. I am happy we did, but I fully expected Beast of Gévaudan to take up the entire season and then cut off right before Misha. This arc was much shorter than Gévaudan and I'm presently surprised with the pacing. While in the manga, there is more focus on Domi's inner conflict, as well as a couple important details about Luna and their relationship to both Vanitas and Misha, I'm content with the adaption of this arc.

I just wish Teacher's reveal was more impactful. In the manga, the way Jun drew this reveal sent chills down my spine. I'm including manga panels below to press my statement:

Moving onto the end. I will not hide it, I love Vanoé. I personally think, be it romantic or platonic, they're soulmates. I think they are what each other need and both help each other to become better versions of themselves. This end scene solidified it, and I was afraid, once I realized we'd be getting this animated, that the team would sugar coat it and not do Jun's drawings justice. I think they did a wonderful job with the material they received and turning it into an animation format.

RATING:

I give the anime adaption of The Case Study of Vanitas a solid 75. I think it is well worth the watch as I think it does a great job being an anime adaption. My only advice is to now go read the manga, starting at the beginning of Beast of Gévaudan if you don't wish the start from the beginning (which I always recommend, no matter what.) I hope more people will now begin to read the manga, and give the support that VnC deserves!