I've used autotools on a ton of my projects, and I like it a lot. I can't speak to any of the problems you had. The one thing I'll say about Autotools is that

I've used autotools on a ton of my projects, and I like it a lot. I can't speak to any of the problems you had. The one thing I'll say about Autotools is that the learning curve is pretty steep, and it took a fair amount of experimentation to get it right on my first Autoolized project. Maybe you never made it all the way over the hump?