I'm with you on this one, alosso. While the current system isn't perfectly accurate, it works for this game. While the current system makes it easier for someone to tier up as a "one course wonder", I don't see a huge problem with it. But then, I don't take the game as seriously as many do around here.
If WGT were going to tweak the current system they would be better served to put a statute of limitations on scores instead of the open-ended time they have now. For example, scores from 24 months ago shouldn't count toward your low score average. That takes into account deteriorating skills due to age and the like, keeping older, more affluent customers with time on their hands in the game. In my opinion, though, that problem is so small that it's not worth investing the time and resource to it. Someone really struggling with that type of problem can just ask WGT to start over.
As "scratch" golfers on this game, you're absolutely right. Rory McIlroy and Tiger Woods don't give strokes when they play Tom Watson and Tommy Gainey in tournaments.
Other than being technically more accurate I don't see a lot of value in changing the score computation here.