As a counterpoint to your sentiment: I am really glad Zotero devs are not spending any time on polishing the UX. I loathe modern user interfaces where a lot of functionality is hidden just for the looks.
Zotero does cover your use case very well and I don't actually see your criticism or UX concerns.
For easy importing of books and papers use the magic wand icon in the tool bar. This allows you to import metadata via ISBN and DOI. Use the FF plugin for importing web pages.
Tags allow you to cluster entries together.
On the right side it is possible to connect items that have a direct connection.
Double click on Pdfs to open them in a Pdf reader that can highlight and annotate. Save the file and use the Zotfile plugin to extract the annotation into notes.
Zotero does cover your use case very well and I don't actually see your criticism or UX concerns.
For easy importing of books and papers use the magic wand icon in the tool bar. This allows you to import metadata via ISBN and DOI. Use the FF plugin for importing web pages.
Tags allow you to cluster entries together.
On the right side it is possible to connect items that have a direct connection.
Double click on Pdfs to open them in a Pdf reader that can highlight and annotate. Save the file and use the Zotfile plugin to extract the annotation into notes.
Zotfile and Zutilo are recommended plugins.