It's not pixel-art. All their "entities" are actually 3d models that are rendered into isometric images. And they've also slowly been regenerating all their images with high-resolution models + renders.
Which makes it better than the 3D you yearn for. You can't do as high-quality and as stylistically consistent graphics with real-time 3D rendering; the computing power simply isn't there.
Pixel art means making a picture while zoomed in to see individual pixels, placing them manually nearly pixel by pixel (only the most basic shape tools are used, and no anti aliasing).
That's funny, for me Factorio has one of the best and well-thought-out UI's I've ever seen in any game (especially for a game this complex).[1]
[1] - With the exception of the circuit network, which is too easy to turn in to spaghetti code and a nightmare to debug.