MayaVi2 is a very powerful and featureful 3D graphing library. For advanced 3D scenes and excellent rendering capabilities, it is highly recommended to use MayaVi2.
mplot3d was intended to allow users to create simple 3D graphs with the same "look-and-feel" as matplotlib's 2D plots. Furthermore, users can use the same toolkit that they are already familiar with to generate both their 2D and 3D plots.
This is probably the most commonly reported issue with mplot3d. The problem is that -- from some viewing angles -- a 3D object would appear in front of another object, even though it is physically behind it. This can result in plots that do not look "physically correct."
Unfortunately, while some work is being done to reduce the occurrence of this artifact, it is currently an intractable problem, and can not be fully solved until matplotlib supports 3D graphics rendering at its core.
The problem occurs due to the reduction of 3D data down to 2D + z-order scalar. A single value represents the 3rd dimension for all parts of 3D objects in a collection. Therefore, when the bounding boxes of two collections intersect, it becomes possible for this artifact to occur. Furthermore, the intersection of two 3D objects (such as polygons or patches) can not be rendered properly in matplotlib's 2D rendering engine.
This problem will likely not be solved until OpenGL support is added to all of the backends (patches are greatly welcomed). Until then, if you need complex 3D scenes, we recommend using MayaVi.
Historically, mplot3d has suffered from a hard-coding of parameters used to control visuals such as label spacing, tick length, and grid line width. Work is being done to eliminate this issue. For matplotlib v1.1.0, there is a semi-official manner to modify these parameters. See the note in the axis3d section of the mplot3d API documentation for more information.
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