Personally I mostly use 3d software to create much of my artwork, even if i'm doing a 2D game. I just work a lot faster in Maya, and if you do a 3d model you can just change angle, rotate and deform it to quickly make more variations. I find 3d much more handy as you can use 3d software to make 2d sprites, or use simple 3d objects as reference and quckly draw pixel or 2d art on it. But starting from scratch, for me making 2D artwork takes a lot longer time.
I think animation in 3d is a lot easier also, but maybe that's just because i'm used to it.
Learning 3d software can take a lot of time though as it's a lot more complex, with modeling, texturing, UV mapping, rigging, skinning, animating, lighting, shaders, rendering. It's so complex in some cases that in bigger development studios, there can be one person hired for almost each of those areas.
2d or pixel art is faster to start with I think, and due to the more retro feeling you can get away with a lot. Animations can be just a couple of frames and a bit choppy, it's part of the charm. It doesn't have to be 30 frames per second smooth animations.
So all in all, I think 3d is more flexible but harder. 2d/pixel art is faster and more forgiving but can still look cool.