Again, after around two months of development, the next version v0.0.3 of matlab2tikz has been released.
The script was extended to support subplots with their exact alignment. This wasn't particularly easy to do MATLAB itself in its plotting routines pulls some ugly tricks to achieve that.
Also, reverse axes are now handled correctly what leads to images now being translated nicely into TikZ/pgfplots.
As a sidenote: I saw some really nice pictures of pgfplots introducting three-dimensional stuff, like, surface and parameter plots. According to pgfplots's main developer Christian Feuers�nger that'll need some more time, but as soon as the release is there matlab2tikz will make use of it. So, get ready for MATLAB 3D plots in proper LaTeX!
For more info and downloads, see the matlab2tikz page.