berickf and I were getting ready to play an M-Engine game (where no player goes 'first'- like with SimulGear) on a WGWF-like RYO! board, and berickf was bemoaning the oft-cited initial position advantage in 2-player games - especially with WGWF. So I created 3 games. We each selected the 2 games we would prefer to play, and the one that was voted for by both of us was the one we played - the other two were terminated.
Of course, it's not perfect. One player has the opportunity to pick from two games where he moves first, and so the game chosen can still be unfair, but there's no doubt that the system easily eliminates the most unfair of starting positions.
One nice artifact: In the cases where it's apparent two boards favor one player, the other player is in the driver's seat, so when those two boards are reasonably fair, that player gets to decide which board he would prefer (or NOT prefer) to play, for instance enabling him to possibly leverage a perceived skill or style of play.
It could be set up to be 3 Eliminate 1 - Same difference.
5 Eliminate 2 would smooth out the advantage even more.
If the site were to try it with Ranked games, the feature could be optional when the game is created.
If both players select (or eliminate) the same game(s) - the site randomly picks from the two acceptable boards.