A couple of differences; Correct me if I'm wrong, is that Zotero doesn't natively allow many-to-many relationships, I sometimes have several different papers, that I am interested in for a couple different reasons, so being able to keep them assigned to different projects at the same time.
Another thing is keeping track of different versions of papers, linXiv has the ability to poll for new versions of the same paper across feeds you setup. I haven't had it come up yet, but it was one of the reasons I started linXiv. Thanks for your comment!