My main problem with Linux today is that some developers still seem to think that all Linux users know how to and want to compile their own software
I agree and if you look at the amount of patches that the packages for Ubuntu or Fedora have to write to get software to compile on their distributions then it will quickly be obvious that it is too awkward to compile from source these days (I blame GNU Autotools for being defective but I digress).
However, this isn't really to do with languages any more. For example, when I had to compile the MonoGame C# binding on Fedora 16, it was a horrible experience!
Much worse than something like the native SDL C library which has been tried and tested on many many distributions and is now extremely portable across them and actually built without any issues.
Though one thing that I thought was cool was the OpenTk Windows .dll worked perfectly on FreeBSD without needing any recompiling. (The best example I have seen of C# being truely cross platform).