Limitation: computing power

3D animation requires a lot of processing power for different processes. The reason CG animation did not appear till the 70's and an animated feature not till the 90's (toy story) was there were no computers powerful enough before then to handle 3D animation. 

For feature films where the levels of detail of the animations is very high and there's a lot of footage that needs to be create the studios have to have what are known as render farms. Render farms are many many computers all hooked up made for the soul purpose to render animation footage. They will have incredibly good components to run them to keep render times down. 

The problem of using/needing very powerful computers is they come at a price, people who don't work for huge studios like pixar or dreamworks may not have these resources available to them. 2D animation can be done with analog components or relatively cheap software that can be run on relatively basic hardware. The "buy in" to have 3D capable equipment may turn potential animators and studios away from using 3D and turn to other types of animation.  

The avaiblity of technology has also dictated the quality of the animation animators have been able to produce. Although early 3D animation has some excellent examples there were severe limitations on what they could produce because of the computing power available to them. A good example is the polycounts available from john lasseter's first animation compared to hyperrealistic character from unchartered 4