The Stinger

The problem, IMO, is that the enemies and other objects are(most of the time) realistic.
The enemies are real photos of people, and not cartoonish like in Duke Nukem 3d.
Point is that if you want them to look good you need a damn good 3d modeler and skinner.
Which brings you to the 3d model to sprite process. It would be a waste to turn such a model into sprites, too much work has to be put in to make such a mode.
Further more, turning every angle and motion into a sprite would take a whole lot of space.
The standard soldier has 91 sprites, which translates into 23mb in high quality sprites.
A 3D model would have around 1mb for the skin(that's really high quality) and 200kb for the model and animations. That's more than 19 times smaller than a good model.
And an other huge problem is that each sprites needs to be loaded into the memory, which takes up a lot of loading time. With a 3D model this would be a lot faster.

So overall, a really good quality 3D model is IMO recommended, it saves loading times and space.