I hear ya, Brian. A real bummer.
I think the basic problem is that the creators of the Gedcom standard failed to take this concept into account when they invented Gedcom and software has simply followed suit. Others who know more about gedcom can tell me if I'm wrong on that score.
Basically, an observer wants to know: "How do we know xx is related to yy in such and such a way?"
The structure I have jerry-rigged to document relationships is to create the following custom facts:
Link to parents
Link to children
Link to spouse
Link to maiden name
Link to sibling
Links to others (aunts & uncles and such)
I put info in the description part of the fact and then attach whatever source citation is appropriate. I often have to enter the fact twice, or three times, for each person (ie a fact for the child and a fact for each parent)
If FTM allowed Shared Facts for others than spouses, one might change these links to reflect that, for example: "Link between parent and child". Then, you'd only have to enter info once - although the second person to share the fact would need to be attached.
Link to maiden name: Marriage record
Link to maiden name: Mary's death record gives mother's maiden name: Johnson
Link to parents: per census
Link to parents: John's death record gives parents: John and Mary (Jones) Smithe.
Link to parent: Named in will
Link to parent: 1) Named a son Darwin, 2) Frank's parents b NY NY per his 1880 census - Darwin & wife b NY NY 3) Jones cousins in his house in 1900
Link to parents: WWI Draft Reg: Lists someone who will know where he will always be as: M.S. Hallock. No relationship shown, but corroborates Merritt Sylvester as father.
Of course, some relationships are more complicated than can be explained in a short description space for a fact. You can either say "See Fact Note" or "See Notes" and carry on the explanation there.
I don't do this for everyone and every relationship in my file; usually cases where it is not self-evident. I try to viusalize what I might think two years from now and might wonder "Why did I think this person was the wife/son/dau/father/mother of someone.
Since these are FTM custom facts, I presume there might be problems in exporting these within individual's data that is exported to other software.