Gotham Knight animation sucks like hell. As for many other batman-non batman animation. I am talking about "animation" not the quality of the series itself. Batman TAS for instance is far better than any Batman movies, in my opinion, Bruce Teem characters design is superb, the screenwriting and direction as well. But the animation (meaning movements, gestures and so on) are very low quality. Most of the western tv animated series (from Disney to cartoon network) are made by eastern countries workers, like chinese, thai, koreans and so on. Mainly for low budget reason. Recentely even japan is delocalizing their animation to less expensive countries.
Animatrix is a collection of short single movies, to make one film. It's totally different than a tv series case, and in fact most of the animated movies and anime have a greater quality. Compare for example Revolutionary Girl Utena movie and Revolutionary Girl Utena tv series. Or Berserk movies and the first old series. I could make hundreds of similar example. With the introduction of 3D animation movie animation has become easier in a way, especially for action scenes requiring special effects. Think about NGE last movies.
But as I said: please, do not compare tv series animation with film animation. There's an abyss between.
Regarding 3D animation: I am personally very tired of it, especially I am tired of seeing 2D animation sacrificed for the sake of 3D reminding videogames, thus being more appealing. The last stab has been Disney closing their 2D animation studios in Burbank and firing all the animators included the historical ones.
As for the 3D per se: I don't understand what's the point of pursueing hyper realism. I watched the last Batman AO trailer (to name one recent) and I am seriosuly not impressed. They pretend to be more realistic than reality? Ok, so where's the creativity? The unique artistic design?
I think that the last Nolan's Batman movies or the Avengers could witness pretty well than combining real actors, 3D and special effects can make an acceptable result. Not to mention than a teaser trailer 3D quality can never be the same of the internal videogame 3D animation and quality (for limits of platforms performance and hd). So in the end it's like a misinformation of a tv ads: the item you buy is different than the one they're advertising. They could tease teenagers, but they'll never tease me, who mind to the substance.