The comparison would be between a Post Reference field to connect two single posts, and a one-to-one Relationship to do the same.
Except, the Relationship is bi-directional, whereas the Post Reference field is uni-directional.
If you connect Left and Right posts together in a Relationship, the Left post knows which Right post it is connected to, and vice versa.
If you instead add a Post Reference field to a Left post to connect it to a Right post, the Left post knows which Right post it is connected to, but the Right knows nothing of the connection.
So when displaying the Left post, you would be able to output fields from the connected Right post, but not vice versa.
With a post Relationship, you could do either.
Relationships are stored in custom tables, whereas the post relationship is simply stored as post meta.
I think Relationships are the way to go. They seem to do much more and seem to be easier if you were to want to expand features using Toolset in the future.