Love plaintext, hate markdown. But it/they is/are what there is. I only use very simple syntax to avoid too many variant problems, and even then I use wikilinks, which aren’t standard markdown (yet).
But I am a files purist. I don’t like to store anything in a database except temporarily.
Not an option since I’m not on a Mac. And iirc, it’s markdown in a database which would rule it out for me again.
Admittedly, most of my writing is done in WriteMonkey 3 which keeps everything in a .json database (enabling wonderful folding control) but I’m okay with that because it also keeps all my data in synchronised files. Which are simultaneously shared with other apps like Obsidian and ProWritingAid etc. Sometimes I might swap backwards and forwards between programs on the same file.
I never took to Scrivener. Tried it from time to time, but it never flowed. I like the company, keep licences up-to-date but don’t like using the program itself.
I put my research etc in markdown files that I access through Obsidian. The wikilinks are virtually instant, and the mix of links and backlinks makes it very easy to analyse what I have. Also have various simple kanbans in Obsidian for a bit more organising and linking.
I’m impressed that you switch easily to Timeline to look things up. I find that too big a discontinuity most of the time. It’s the very different interface probably; doing something bigger is fine, but something small is an irritation when I can get it with a couple of clicks when it’s in Obsidian. I don’t use my iPads, but Obsidian works well on my Android tablets.
The planning and creating ones are important. I’m never completely convinced it’s not just inefficient procrastination and I would really be better off with just one, but I find them all different and I make progress in one, when I don’t in the others. At times I even use a simple outliner. It’s whatever helps me best to sort things out in my head.