Pretty amazing submission. I have only had a few minor issues with it:
1. There is no way to provide extra axis options (e.g height and width) for each subplot. This is especially needed when you have a few vertically stacked subplots with a common x-axis and you want to remove the x-axis labels from all subplots but the bottom one, or you want different heights from each subplot.
2. It needs a better (smarter) downsampling algorithm. Currently, it is very easy to hit TeX memory limits when you have a large number of points (see http://tex.stackexchange.com/questions/59562/matlab2tikz-tex-out-of-memory/66831#66831)
3. It cannot properly convert time graphs that are automatically generated by step(), impulse() functions and the like (from control system toolbox)