Some people have the wrong idea that 3D is an evollution of 2D, while actually, they are just totally different mediums and as such can´t be compared equally. One can´t be "better" than another just because one is 3d and the other is 2d. Just as with games.
I love 2d animation, I have probably seen every Disney thing under the sun when they used to do 2d for either cinema or tv, the first time I heard a computer was getting involved in an animated movie, must have been in "The Lion King" when they used it to drive the antilope trajectories during the stampede scene. And when they stopped doing animated movies, I turned my sight towards Japan.
There are a lot of awesome and plain ugly 2d animations, and awesome and plain ugly 3d ones from a technical point of view.
I recall watching "Beast Wars" in Cartoon Network, it was an example of the improvement 3d had. The first season had almost plain looking textures, harsh animations, simple backgrounds, etc. The second season, improved quite a bit and on the third one you had a total overhaul. I loved it since I love anything with robots, but, I would watch Gundam Wing and enjoy it as much.
Also when I watched "Ghost in the Shell" I was awed by the animation.
And then, there are the 2d/3d amalgamations like
"アップルシード" which try to look 2d while being 3d, others that mix 2d with 3d elements and give it a 2d look that when done right blends in just nice.