There are two things I really dislike.
1) Usually who ports MS Windows software for Linux doesn't care about quality. You can see bad behavior and / or bad looking. Matlab, for instance, has a nice look and feel on Windows but its Linux version is too ugly. It seems that some beginner was in charge of Matlab's port.
2) It seems that on open source software everyone wants to create its own application. It doesn't matter if there are other applications that do the same.
During my research time on mathematical and statistical software to use instead of Matlab/Simulink I found out a giant list of software. And know what? None of them is as good as Matlab/Simulink. They are not even as easy as Matlab/Simulink.
I'm not saying these software aren't good. I'm saying that they cannot compete because Matlab/Simulink helps you develop your solutions in a very easy, robust and intuitive way.
No one wants or can spend time with incomplete tools or tools that make life difficult for user. In short, it is very difficult to convince an engineer or a mathematician to use free software.
I would like the brilliant minds working developing free software for mathematics come together to develop a single mathematical software. So this software could compete on an equal footing with commercial programs.
There are two article that express this better than wrote on these to articles: Why Free Software has poor usability, and how to improve it (by Matthew Paul Thomas) and http://ometer.com/hacking.html (this article was written in December, 1999 but is very up to date.).
Bellow you can see three links that contains lists of programs, plotting software and libraries that are related to math.