It's up to the developers, not the tools
I switched from C/C++ to Java a couple of years ago. By now I'm a happy ant user, always having a slight shiver running down my spine when thinking of the make mess in my previous developer life. Getting started with a reasonably developed piece of Java is a matter of having the right JDK, ant and cvs installed on whatever box you have, and typing 'ant' (ok, may be after editing some weird build properties...), and it is made both for emacs-fans and IDE softies.
But nifty tools cannot help you if the developers don't take care for proper versioning and compatibility issues. Open source Java programming by now suffers from the same versioning mess. It's a CLASSPATH nightmare to have to maintain a single Servlet engine with a few webapps using a few common open source frameworks.
Nevertheless I think autoconf/make etc. should be praised, put into the shrine of great old software, and then a modern build system should be made ;)