The nature of thoughts are non-linear, inter-woven.
Thoughts are a map of associative thoughts, epiphanies, questions and answers.
A tool for thought in the form of natural language should expand your working memory, letting you construct and navigate in your idea space with the least effort.
You should be able to trace the origin of your thoughts, push it in any direction.
You should be able to mark different thoughts with different colors, such as questions, answers, questions without answer, most critical insights.
You should be able to connect the thoughts together freely.
You should be able to share it with others (including AI), and discuss about the assumptions you made in each thought.
Linear Documents
Prevent you from seeing the structure of your thoughts.
Mind Maps
Force your thoughts to be centralized, restraining you to think freely.
A space of connected thoughts, with full keyboard navigation is what you need.