A few years ago, I created Markdown Notes with the same goal in mind. Markdown with LaTeX formulas and graphs was a powerful tool.

However I eventually left university and stopped using it. Then I started using paper and pen to great effect. I can draw in seconds what I can type in minutes. Now I use Notability on an iPad Mini. Same thing but with better editing tools.

Frankly, I just like pencil notes a lot more than text. It just works better for free form thinking. Immediate and short-term convenience is more important than having my notes in text files.