• make(1) has a hard time rebuilding target files when source files have changed. The problem is that users have to declare the dependencies of a target before the build, but due to file search paths, it can be that dependencies are only known after building a target. To know about all dependencies, make(1) would have to build any target at least twice.
• make(1) by default does not rebuild a target when its build rules change. While this seems really weird to me, it seems to be a consequence of having a single makefile. When a build rule is changed, the makefile changes. So should all targets depend on the makefile implicitly? One could argue that they should – but then each change in a makefile would rebuild all targets.
• make(1) can not handle non-existence dependencies. Imagine a file foo.h being searched for by a compiler in directories bar and baz (in that order). If the header file baz/foo.h is found, then bar/foo.h should be considered a non-existence dependency: If at any future point in time it exists, the target should be rebuilt.
These problems are all solved by DJB's redo approach, which I implemented in a few hundred lines of Bourne shell (/bin/sh): http://news.dieweltistgarnichtso.net/bin/redo-sh.html