The issue you described of having same amount of game and match wins and yet somehow having less points has already been taken care of with the scoring adjustment. You can no longer have the same number of game and match wins as another player and not be tied on points.
In a thread about alternatives to the current system you aren't sure why best out of 3 is being brought up? Wouldn't that fall into the alternatives to the current system category?
But you can currently have the same amount of game wins and end up on different points.
If you go to a 3rd because of luck, sure you can make up for it, but if you go to a 3rd because your light side sucks vs that particular dark your opponent has, then its luck if you have to play light or dark. Unless of course by best of 3 you mean 6 games. Then you will just create a huge length for games and a very long event.