Right, the system() function in C, which PHP probably uses, and is os.system() in Python, is DEFINED to run /bin/sh. You never know when a program might call it (although I agree it is almost always bad practice to use it -- use fork/exec instead.)

So basically you should never make /bin/sh fish, because then you will no longer have a Unix system (according to POSIX).

That's just lazy programming, and if anything, we should have more incompatible shells so that developers will start to write their programs to stop shelling out and run individual programs, or if they do shell out, actually declare the shell you're using at that point and don't assume it will be sh compatible.

Personally I leave bash as my login shell and just set my terminal emulator to launch fish on startup.