I always had a strong dislike of commonly used build systems. There's always something that would bug me about those I had to use or interact with.
Autoconf/Automake/Libtool are complex, slow and ugly. Custom, weird macro language? Check. Makefile lookalike with different features? Check. Super slow single threaded configuration phase. Check. Gigantic, generated scripts and makefiles, full of compatibility code, workarounds for dead platforms and general feeling of misery when something goes wrong. Check. Practical value for porting between Linux, MacOS and Windows. Well, sort of, if you want to endure the pain of setting up the dependency chain there. It feels very foreign away from GNU.
Autotools were the first build system I've encountered. Decades later, it's still remarkably popular, by both broad feature support and inertia. Decades later it still lights up exactly one core, on those multi-core workstations we call laptops. The documentation is complete but arguably cryptic and locked in weird info pages. Most projects I've seen cargo-cult and tweak their scripts and macros from one place to another.
Despite all the criticism autotools did get some things right, in my opinion. The build-time detection of features, as ugly, slow and abused for checking things that are available everywhere now, is still the killer feature. There would be no portable C software as we know it today without the ability to toggle those ifdefs and enable sections of the code depending on the availability and functionality of an API, dependency or platform feature.
The user-interaction via the configuration script, now commonly used to draw lines in the sand and show how one distribution archetype differs from the other, is ironically still one of the best user interfaces for building that does not involve a full blown menu system.
The theory where you don't need autotools to use a project built with it. The theoretical portability, albeit to mostly fringe systems, is also a noble goal. Though today I rarely see systems that don't rip out the generated build system and re-generate it from source, mainly to ensure nobody has snuck in anything nasty into that huge, un-auditable, generated shell monstrosity that's rivaling the size of modest projects.
Will autotools eventually be replaced? I don't think so. It seems like one of those things that gets phased out only when a maintainer retires. The benefits of rewriting the whole build system and move to something more modern must outweigh the pain and cost of doing so. In the end it would help to modernize autotools more than it would help to convince everyone to port their software over.