I got the same problem and posted my question in this forum 
http://www.developpez.net/forums/d836964/autres-langages/python-zope/calcul-scientifique/matplotlib-scatter3d-colorisation-fonction-z/
(here)  a few days ago... My question receives a lot of visits but no
reaction however I think it may be an important information for people
wanting to use matplotlib efficiently. Please let me know if you can find
anything about it :confused: Even if everything works perfect with 2D
scatter I can't solve this issue with scatter3D. Knowing that's it's a bug
should already be a nice answer...

Luc Estebanez wrote:
> 
> Dear All,
> 
> I am trying to use the new 3D facilities offered by Matplotlib.
> I know the mlab module of Mayavi, but I am interested in the vector 
> export facilities offered by matplotlib.
> 
> Here is my issue : I can't manage to vary the color and/or size of the 
> markers when doing 3D scatter plots :
> 
> fig = plt.figure()
> ax = Axes3D(fig)
> ax.scatter([1,2,3],[3,1,2],[1,2,0],c='r',s=[4,10,20])
> 
> The code above doesn't show size changes for each marker, just like :
> 
> ax.scatter([1,2,3],[3,1,2],[1,2,0])
> 
> Does anyone have an idea of what is going on ?
> 
> Thanks a lot,
> luc
> 
> (I already posted this issue on the user list, but it seems to be a bug, 
> and no one their seemed very interested in this  issue either...)
> 
> 
> 
> ---------------
> luc Estebanez
> Graduate Student,
> ENS, Paris
> 
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