This article gets at something that's really key. The system is so much more important than the tool. The tool may facilitate the system, but without a system even the fanciest tool won't help you feel organized.
and even if you are able to momentarily capture the complexity, ideas and requirements in your mind evolves so fast that your solution is immediately obsolete.
I'm not sure what this curse is called in the software development industry, but I see no solution to it.