Favorites are publicly viewable, not everyone may want that.
I use upvotes for bookmarks as well. The interesting thing is that these upvoted bookmarks are private unlike favorites.
I tend to upvote too many things for the upvoted list to work for me, so I'm glad the favourites function exists. If I find a comment useful or insightful, I automatically upvote it without thinking. Maybe I upvote too much; I don't know.