You hit the nail on the head. A well designed system has coherent building blocks. When you scale that up, you don't end up with a rat's nest. Funny you should mention Evernote. I'm building https://histre.com/ as the said coherent alternative to it (among other reasons), as Evernote truly turns into a hoarder house after a while.

I'm a big org-mode user as well, and that solves most of the "write stuff down for later" needs for me.