I think Obsidian is lonely at the top, right now. Zettlr is solid, but replicating the Obsidian experience is nearly impossible with it. Anytype is better at that, but it's "smaller", and probably more suited for daily notetaking, not to build your super-customized writing environment for long-form projects. (Like your MA thesis, or your dissertation.) Finally, Logseq, on paper, is pretty great - but, speaking from my own experience, it has shown to have problems on some Linux versions like Manjaro.
TLDR - Zettlr is my favorite alternative, as is. Logseq would have that spot, though, if it worked more smoothly.
I actually like that, and I like this about the Fediverse in general: Nothing wrong with YA-oriented media, but I'd rather limit my own online time to stuff - and to a level of debate - that ideally is oriented exclusively towards the topics I'm most interested in, personally.