In a 3d environment, sprites have systemic issues regarding viewing angles. If a bad guy runs directly at you, or at you from a 30 degree angle, he looks exactly the same. Models convey more information than sprites do about their environment.
This isn't a blanket statement about models and sprites, but given a free camera and a 3d world, I think models work better. They don't have to look better, though: I'd say that Quake looked a lot worse Duke3D, even though they were both released in '96.
In terms of aesthetics, I'll freely state that I find the model to be more attractive than the pixel art. That's not to say that 3D models are always superior. I love pixel art. I think the old, 2D Sam & Max looked a lot better than the new, 3D models that Telltale Games are using. Still, the creator of the cacodemon model actually strikes me as the better artist. Also, it's not because it's new or fresh. The 3D model looks almost quaint compared to most modern productions. It does, however, strike me as more malevolent and sinister, possibly due to the shape of the mouth and the relative size of the eye.
For the record, I'm not posting this as a critique of your tastes. I just wanted you to know that some people really do find that model to be objectively better.
Unfortunately with a lot of these fan graphical enhancement mods and addons, the content creators lack sufficient knowledge of visual/art styles and experience applying them.
This deep understanding of game art is necessary to successfully translate a particular 2d art style into 3d, or suitably reimagine it in a more 3d compatible style.
I wonder if it's possible to get this old image of Cacodemon and make bigger nice one with that technology of depixelization which was on front page yesterday (or was it two days ago?).
Is it just the "it is something different/new and thus feels fresh" or do you really consider it look better objectively?