I think a question people should often ask themselves is: Have you considered if you need a build system at all? Is this something I can properly build with a plain old Makefile?
It's possible - I can't say I gave it much consideration, I just used automake because I knew about it and it's widely available.
I shouldn't need to include autogen.sh or require people to have automake/autoconf installed to build it, but I had problems using a configure script/Makefile generated on one system on another. I guess I'll sort it out when I come to understand the tools a bit better.