Don't get me wrong, auto* was (and still is) a tremendous improvement over the bad old days of hand-editing makefiles just to have a chance of having your software build. But it is well past time to have designed, implemented, and deployed a better alternative, and I don't see too many good signs of that.
What's wrong with it? Let me enumerate the ways:
1. It's way too complicated. Good software and free software, not to mention good free software, run on simplicity. auto* does not have this quality.
2. It's implemented in bad languages. One bad language would be enough, but M4, (portable) make, and portable shell? There's a good reason nobody else has even attempted writing an app in that combination of languages.
3. Original goals are no longer very relevant. In the bad old days, there were lots of vendor Unices and other strange build environments. Today, in the *nix world, there is just the GNU toolchain. The amount of actual diversity that needs to be configured around is minimal.
4. It doesn't solve real-world portability problems. For many users, getting programs to build on Windows is at least as important as compiling on an ancient MIPS running Ultrix, yet auto* isn't much help at the former.
5. Bad error reporting. In "configuration science", one of the overriding goals should be production of clear and meaningful error messages.
6. Lack of overall systems thinking. Much of what auto* does is work around limitations in tools such as sh, make, ld, package managers, and the like. If some of these other components are better places to solve configuration and build problems, let's do it there rather than twisting ourselves into pretzels trying to work around them. Apple had the guts to extend ld in several important ways, including two-level namespace support. Why are we still stuck with the clunky late-'80s approach copied from old vendor Unices?
It's been clear for a long time that CVS needed replacing, and now we have a variety of great alternatives, some of exhibit that classic, simple, do-one-thing-and-do-it-well free software philosophy. We should have something similar for the problems that auto* solves.
I find myself posting from Japan once again. Why is it that I'm more likely to find a free moment here than back at home in Berkeley? Anyway, it's nice and cold, and I even got to see some snow up north in Matsumoto.