History on relationships

Here is one thing you can do.
Using GDM, create an MDA Custom Object with the following fields
        Relationship ID; Date; Field 1; Field 2;....Field N
Where Fields 1-N correspond to the Relationship fields that you want to track history for.  Then create a very simple Rule that just queries for Relationships with whatever filters make sense for you and then use "Load to MDA" to insert the current values and the date.  You can create a schedule to run the rule daily (or whatever makes sense).  
This gives you a very nice history tracking of the values you care about.  Be aware that it does not necessarily capture every change since you might change the value twice in one day.  
You probably should also put in place a Rule to purge the older data.  Again very simple: once a month or whatever, delete records where the date more than 90 days ago, or, again, whatever makes sense for you.