I left Evernote and settled on OneNote for my notes/planning replacement app. I ran into a number of things that were problematic, including incompatibilities between platforms, but didn't discover the biggest problem until I decided it wasn't for me after two years.

There is no way to export from OneNote. If you want to get it into another system, you can't. If Microsoft decided to pull OneNote tomorrow, there would be no way to get all of your information out of OneNote and into another system.

I agree with your conclusion that there's no one solution, it's the combination of tools that works for us. In the end, it's the tools that allow the process to become smooth and effortless (or as close to it as possible) not the ones that require constant tweaking.