For a long game it is very hard to organize 6 players to play consistently under the best cirumstances. The Greek guys used to organize competative games and ran into many problems with people not showing up. Many games ended because one team stopped showing up or one player could no longer make his commitment to the game.
There system as based on each team playing Axis once, and Allies once. If both sides won one game, the side that lasted the longest before annex became the winner. That kind of thing.
I think that if you are going to set up a competition it would be best to set up a "round robin" system, the kind used in international football most often. You start with several teams of 3 playing a pairs of "short games" from 38 going to 41, with specific victory conditions. The intitial games are 2 v 2 with the third player being "alternate sub". This way the first rounds are short, and if there is a problem with players the team should be able to have a substitute player available.
Each team would play each other twice per round, onces as Axis, once as Allies. Most preferable too would be having the host be a neutral country, not one of the players. Each pair of games would count as a match with a point being awarded for the match, not the individual games.
Only the final pair of games between the final contenders would be a pair of long 36 games with a full group of 6 players.