I think the most annoying issue is that for larger software with lots of options and dependencies, running configure just takes a long time (especially before SSDs where a thing), and will terminate with exactly one error. Getting past ./configure could take literally all day.
This made me think back then that someone could fix autotools by caching tests results for a specific system. Why not me? So I opened its sources... and closed it. No positive outcome could recapture the time required to even understand what’s going on in these scripts.
Agreed that this is an annoyance. Autoconf-generated configure scripts are definitely slow, mostly because they test a ton of things that probably don't still need to be tested.
The overall system still provides a ton of value and a lot of relevant tests in addition to the not-so-relevant ones. After years of writing increasingly complex Makefiles to test for this-and-that, Autoconf was a breath of fresh air for me when I made the switch a couple of years ago (even with all of its crustiness).
