I’ve found that it depends on what you need to do with the text. That’s hardly a novel insight on my part. 
I often require multiple heading levels for longer articles, so having a clear outline of the text is helpful. I also include a significant number of citations when summarizing or quoting from other sources. Occasionally, I need to insert tables, charts, or images, which are much more difficult to work with in plain text.
I’ve used Ulysses, iA Writer, and several other writing apps extensively. Each has its strengths and weaknesses. At present, I’m experimenting with drafting all basic text in Apple Notes. With the addition of collapsible headers, I effectively have a built-in outline view. This makes it easier to navigate longer drafts and manage document structure without switching apps or formats.
With OS 26, Apple Notes now supports Markdown import and export, allowing greater flexibility if and when I need to move between plain text and rich formatting. When more advanced formatting is needed, such as applying custom paragraph styles, I open the note directly in Apple Pages. The headers are automatically converted to the appropriate formatting styles, streamlining the transition from draft to final document.
There are multiple advantages to this approach. Apple Notes offers immediate access across all devices, fast and reliable iCloud syncing, and integration with Apple Intelligence for grammar and style suggestions. I can insert tables, images, scanned documents, and handwritten content.
For version control and archiving, I store the original draft text in an archive folder within Apple Notes. Once the document is finalized in Pages, I export it as a PDF and import it into DEVONthink for long-term storage.
The exception is my book project, which I’m writing exclusively in Scrivener.
Finally, everything is native, and no additional costs are incurred. 