Agreed. MATLAB its set of downsides. On the plus side development is rapid and since 2008 it has good support for classes. We're starting to move toward python for future work.
I think MATLAB itself isn't so bad, so much as the way its typically used -- poorly commented, organized, and untested. We put a lot of effort into clearly commenting and organizing the code. We used matlab-xunit and hudson to manage testing, which worked quite well. http://www.mathworks.com/matlabcentral/fileexchange/22846-ma..., http://www.mathworks.com/matlabcentral/fileexchange/33971-xm....