I think Outliners are great for thinking and note taking.

For me tools to help me think usually means those that help in writing. Writing is thinking on paper, giving it a tangible form. You write after spending considerable time distilling your ideas and assumptions to a coherent form. However, the problem with writing is that it is time consuming. Anyone who has written more than a paragraph will attest that the important part of writing is to whittle away all the flab by editing to make your ideas clear to your audience. To make things clear often the writing needs to be reorganised because the vision of the writer can't always be conveyed successfully to the reader without considerable skill from the writer.

Outliners helps in this organising aspect. In a wordprocessor or text-editor you work with logical units of sentences and paragraphs that carries multiple ideas. It is not easy to mix and match stuff there as you need to rewrite them often which can become tiring. With Outliners, you can, in a way, do that. Incessant focus on features to reorganise ideas aid in creating logica arguments. Clarity comes with having an understandable structure. Outliners let you tinker with the structure without much cost. In a wordprocessor, cutting and pasting becomes tedious after a while. Outliners are built for moving things around. It is comparitively easy to move text around. Keyboard shortcuts are tailored to allow you to do it easily. It becomes second nature after a while and you feel constrained using any other tool.

Outliners use each line/bullet as the smallest constituent of the 'document'. It can be heirarchichal or it can be flat. Bullet points allow ideas to be concise. You can divide ideas to make small sub-chunks while your brainstorming sessions progresses. These programs allow them to be moved around and edited to make them fit with the idea you want to communicate. SInce each lilne only contains only one idea, it is easy to move them around without much editing. Good outliners (single pane outliners) allows features such as 'hoisting' (hides everything except the current idea under consideration) and sorting features to make thought creation and organisation a breeze.

Many 'outliner people' [0] will have a brainstorming session to get everything they have in their minds out in the open. Later they rearrange them in to heirarchies (paragraphs/headings) to make sense of them. You can sort, resort and arrange your ideas in whatever way you like.

Many people use this together with similar other tools like Mindmapping software, which accepts OPML file format as input, allowing work to be transferred seamelessly to tools that are best for the job.

It is sad that outliners are not seen wide adoption among people but they were big in the 90s and many were hit products (Thinktank, More, Maxthink). I can't even find good outliners now for Windows. Some exist for Mac (Omniouliner). Although I am a user of Org-mode in Emacs, it is not useful as a thinking and brainstorming tool as it doesn't have the ability (out of the box; anything is possible in Emacs) to move around stuff easily as in a dedicated outtliner.

[0] https://www.technologyreview.com/s/520246/as-we-may-type/