Now that there seems to be a system in place that does a fine job of tracking the relationships between a game and its expansions, how about allowing users to track plays of expansions simultaneously with main game entries? Something like an addition to the interface with checkboxes for all possible expansions which, when checked, records identical details to the play of the main entry to a play of the expansion(s) that were checked?
That system allows this user-created script to work:
Pops up for you when you go to log a play of the base game. Not officially supported by BGG, but works nonetheless. You can read about it here: SPLU