That programs and libraries get installed in a consistent place is nice in some ways I guess, but for me it's always been terrible, since it's more often than not really hard to install multiple versions of the same program or library (and therefore two programs using different versions of the same library. The hairier programs can't even be built from sources on "the wrong OS version" by most mortals, not to mention installing binaries; try building KDevelop 3 on an OS where only KDevelop 4 is made available by default.)

Another maddening thing is how Linux distributions can't agree on where any bloody thing is - even env, which in large part serves a workaround for the inability to count on absolute paths, is at /usr/bin/env on some distros and /bin/env on other distros. So is something as basic as tcsh. How to write a portable tcsh script in these conditions I don't know. (And "you should use bash" misses the point, and also brings fond memories of #!/bin/sh script breakage when it turned out that sh is bash on some systems but dash on others.)

Bill Gates said in the 80s that there are many different Unixes and this will remain a problem for a long while. Damn, did that man make a good prediction! As to Linux - Richard Stallman said that it's a kernel, not an operating system. Damn, did the various distributions go out of their way to prove him right, creating many different, not Unixes, but Linuxes!