I don't know anything about the internals of Quest data files, but my suggestion would be to allow expansion authors to have the option to let their expansion just scale in difficulty compared to the players level.
This would mean someone can create an expansion and not have to worry about whether its meant for level 40+ or a brand new player. Will lead to more expansion sales surely
But its optional only. Authors could still pin their expansions (which is kinda how it works now), and this might be relevant for the Hero of Lukyamore series etc.
My other suggestion would be to make the main base game quest an expansion (which is bundled but not automatically started).
The base game would be little more than a small area with a few vendors and a port allowing you to travel to whichever expansions you did want to start (including the bundled base game one)
Having now completed Quest base game on Palm Pilot, Pocket PC, iOS and having bought iOS HD, I just cant face having to play the Matras story arc for a fifth or sixth time.
Not that Quest II will have the same Matras base game, but it would be nice not to have a similar issue in the future.