I skimmed the comments quite quickly so I may have missed it, but it seems that nobody has mentioned what I think is one of the biggest issues with make (as actually used, as opposed to some ideal): recursive runs. I have seen several packages (and I used to work with one rather large code base) which were subdivided into multiple directories, sometimes in several levels, each with its own Makefile and some rule that did

  for d in $(SUBDIRS); do cd $d && $(MAKE); done

A top-level make run would take ages just to recurse through everything to decide that nothing needed to be done, and dependency tracking did not work across modules, so the only way of making sure you got everything rebuilt was to ‘touch’ everything. (The advantage of the setup was that you could check out just part of the tree and build it separately.)

It would be really nice if make could read all subdirectory Makefiles, build one global dependency graph and then have at it.