Ulysses has been my world since 2003. The upgrade from version 2 to 3 was massive, but totally worth it, even though it meant a lot of work for me initially, as I export to LaTeX, which was easier under version 2 than it is today. (You now have to rely on Pandoc for conversion, which has its bugs.) There are advantages too: the markdown method means that it is easy to export to a variety of formats from Ulysses, easy to sync (as markdown files are tiny, unlike Word or PDF files), and everything is designed in a very non-distracting way, leading the pack as far as I'm concerned by quite a distance. I write daily in Ulysses, so I dod not hesitate to subscribe: I'd rather have a viable business model for the software I use for a living.
The shortcuts are great, the design is great, there's nothing I do not like. Yes, I preferred version's 2 filter mode instead of the tired folder structure, but I can live with that concession to normality ;) especially since footnotes have become so much more user-friendly.
Note-taking I still do in Tinderbox, my other staple software, which I use in tandem with Ulysses every single day.