Side bar, I know a lot of people are saying "time to scrap autotools for good, everyone should just use cmake/meson/GN/Basel/..." I have a couple different responses to that depending on my mood, but the important one right now is: Do you honestly believe that your replacement of choice is *enough* better, readability wise, that folks will actually review patches to build machinery carefully enough to catch this kind of insider attack?
On the subject of implementation language, I have one half-baked idea and one castle in the air.
The half-baked idea is: Suppose ./configure continues to be a shell script, but it ceases to be a *generated* shell script. No more M4. Similarly, the Makefile continues to be a Makefile but it ceases to be generated from Makefile.am. Instead, there is a large library of shell functions and a somewhat smaller library of Make rules that you include and then use.
For ./configure I'm fairly confident it would be possible to do this and remain compatible with POSIX.1-2001 "shell and utilities". (Little known fact: for a long time now, autoconf scripts *do* use shell functions! Internally, wrapped in multiple layers of M4 goo, but still — we haven't insisted on backcompat all the way to System V sh in a long, long time.) For Makefiles I believe it would be necessary to insist on GNU Make.
This would definitely be an improvement on the status quo, but would it be *enough* of one? And would it be less work than migration to something else? (It would be a compatibility break and it would *not* be possible to automate the conversion. Lots of work for everyone no matter what.)
On the subject of implementation language, I have one half-baked idea and one castle in the air.
The half-baked idea is: Suppose ./configure continues to be a shell script, but it ceases to be a *generated* shell script. No more M4. Similarly, the Makefile continues to be a Makefile but it ceases to be generated from Makefile.am. Instead, there is a large library of shell functions and a somewhat smaller library of Make rules that you include and then use.