The install was a breeze because you practically installed a self contained black box. What if you wanted to use Apache instead of nginx or a custom compiled Python interpreter or PyPy?
How often do the majority of people need to make these changes? With a well designed "self-contained black box" it should be possible to make the changes you suggested (web server and Python interpreter) pluggable, to some degree. There is always going to be a trade-off which has an impact on those with more specialized requirements.