Much depends on what the final output is to be and if Scrivener’s text-tidying and compile tools are needed. If you’re working in markdown and compiling your documents outside Scrivener, you probably don’t need Scrivener at all. If you prefer markdown, have you tried Obsidian?
It is just over a year old and still in beta, but it already works on more OS platforms than Scrivener, is more powerful in most aspects than Scrivener—thanks to its growing array of smart plugins, is markdown based, and uses a future-proof format that is easily accessible through the file system and which can be edited by other apps at the same time, giving users limitless control over their writing and how it is stored, accessed, and edited on multiple devices. On top of that, it is free for individual users.
Some Scrivener exiles have already switched over completely. I’m still using Scrivener occasionally, mainly on legacy projects, but I think that with the trajectory and speed of development of Obsidian, my need to use Scrivener (if it remains unchanged) will diminish to pretty much nothing more than occasionally taking a nostalgic look at an old ally. And I have used Scrivener for Mac since it was in beta.
I do most of my work (say 95%) in scrivener and don’t see that changing. Sometimes I get an idea and write on my tablet, but not that often. However, I read books, articles etc with my tablet and take extensive notes that I want to get into Scrivener to incorporate into my work. I don’t want to see the MD when I edit my work and review it. I want to see wysiwyg because its easier to read and see about what the article will look like, or scan the report. I also grab website pages with the Joplin web clipper. I had used Evernote, and switched to Joplin.
I was in the same boat until a some months ago when someone posted on the forum about using Bear. I tried it as a writing environment and loved its clutter-free interface and beautiful typography. From Bear, I found Obsidian, and some of its features just fit better with my current needs: markdown; you can have WYM and WYG panes beside each other, with the WYG pane updating in real time as you type in the WYM pane (a WYG editor, like Typora and Panda, is coming soon); live transclusions; iframe embedding where, for example, you can embed a steaming video in a markdown file and then watch the video and make notes in the same file at the same time; linked scrolling, so that you can work in two panes simultaneously and keep them aligned; multiple cursors; automatic backlinks; the ability to have the same file open in a different program without having to shut Obsidian down; and so on.
For my needs, it also very fast in terms of syncing markdown files through iCloud and having the freedom to make changes to multiple files quickly. I have been working on a project that has just over 900 small files, of about 50–300 words each. In Scrivener, a search and replace across all the files can take several minutes to complete. With the same files output to markdown, I can use Atom or a similar text editor and do the same search and replace in a few seconds.
The speed, efficiency, and added features mean that I am in a happier and more productive writing environment. And I always have Scrivener as an additional tool if needed.
I have used Scrivener to write scientific papers for quite some time and IMO it is fantastic when sequentiality is required. However, I struggled to find a proper long note- idea manager: Scrivener, Evernote and Devonthink worked to gather notes but did not help me much to retrieve information or connect ideas because neither tags&metadata nor folders worked out in the long run. Obsidian represents an epiphany: a dynamic network able to show structure but no restricted by hierarchy, a personal wiki with visual aids. Thus, the graph view has revolutionized my workflow, I can now easily visualize hundreds of notes and identify orphans and relevant nodes. Contrastingly, corkboards and outlines appear so limited now.