I’ve just discovered this forum while searching a way to smartly organize papers and idea for my engineering thesis for master’s degree. Today I use Joplin as general purpose note-taking but it lacks many linking feature for now. I found Liquidtext (https://www.liquidtext.net/) (Marginnote (https://www.marginnote.com/) is similar but only for Apple ecosystem, not my case) and there are many nice ideas in it. You can create mind map with excerpt of multiple documents and immediately go back to the specific paper. But it lacks bibliographical feature like Zotero.
The major pro is that you can use also image excerpt that is impossible (right?) with Zotero and is important if you want put into the annotation an equation. I also saw that Margin Note support flash cards and it could be very useful for memory.
I’d like to know if you know those programs, what you think about, how you use them, if they are compatible with zettlekasten method and Obsidian. I think you could use Liquidtext and then export to obsidian but I don’t know.