They are sort of aimed at different ends of writing. Ulysses is a great writing tool, and thats what it provides a simple writing environment. Scrivener is at the other end as in it lets you manage your writing project from research to writing to publishing in different formats (PDF,ePUB, DOC) etc.
If you do any programming I would say Ulysses is sort of like SimpleText and Scrivener is more like a full blown IDE.
To take a fiction example. Scrivener lets you break down your writing into book, parts,chapters, scenes in chapters (or POV of a character). Lets you tag individual sections with metadata. And see just the flow of a specific tag (I.e. saying show me the story arc off all pieces tagged with this characters name will show you the continuous text of those pieces so you can hone a story arc).
Can let you rearrange scenes by moving them around so you can change them sort of visually if you want to change the flow of the story etc.
I am just scratching the surface of the features here.