missed point - cross development
You didn't mention one major deficit in autoconf and friends. They don't play nicely with cross-development environments.
Cons is a solution ? I can't agree.
Having used cons for two years I can state without equivocation that it is powerful, and works reasonably well, but somehow every project that used cons ended up with massive conscripts that looked ... aweful. Classic spagetti code where an apparently innocuous change in one spot creates havoc due to hidden side-effects.
I believe there is too little structure in the scripting language. It's the write-only language problem.