I am not a developer. But, I can see the difference between the two applications.
Zotero is supporting Bibtex format quite recently; mostly using addons. The bibtext is the main focus of Jabref. Jabref doesn’t attemp to insert references to word processors like Zotero does.
So, they are different with different audience. Jabref and BibDesk are primarily for Latex (bibtex). Zotero and Mendeley are primarily for word processors like MS. Word.