Autotools (the ./configure) is generally a pain to work with. It essentially spits out a massive script and incomprehensible makefile that allows your program

Autotools (the ./configure) is generally a pain to work with. It essentially spits out a massive script and incomprehensible makefile that allows your program to be used by the three people who still run HP-UX or AIX. Good makefiles are simple, and should Just Work™. The dependencies should (theoretically) be listed in the project documentation, though it often isn't. Package managers are definitely better for non-developers, though. Build systems generally aren't geared toward regular users, so users will find them confusing.