Regular users are not supposed to install software like this. The only sane way to administer a distribution is to make sure everything passes through the official package manager. This leaves the developers and package maintainers to deal with autotools and I don't hear them complaining (very loud[1]).
Autotools is simply good enough for the job and instead of being some sort of hated legacy it's being sometimes preferred for new projects (cough [2] cough).
[1]: https://blog.flameeyes.eu/tag/autotoolsmythbuster/
[2]: https://github.com/stefantalpalaru/vala-skeleton-autotools