My problem with a race style format is that players need opponent, and if each player wants to advance his own 'track' then he will be less willing to play games that are on his opponents track. For instance, if I and my opponent are both one game away from our finale, then who's game do we play? No matter which game we play, the other player feels like he lost due to an arbitrary timing issue or dice roll rather than because he was out played.Real life and real life politics too often get in the way when there are prescribed scenarios to play. Especially if those scenarios need to be fought against particular opponents. I know if my roster is being unkind, I can be out of action for a couple of weeks and it's not fair that the whole campaign grinds to a halt because one player needs to run a finale game against me.
This is a pretty insightful and valid criticism; this is something I have also thought about and have some mechanisms in place to counteract. As far as picking missions, the two main factions in the game alternate picking missions, so there will be an equal distribution of missions run by either side. It's not so much an arbitrary timing thing as it is a regular rule in place for the whole campaign.
As far as players being sore losers and opting out, that is a lot harder to regulate. right now, the steps to setting up a game are:
Find opponent
See which faction it's turn it is to pick a mission
Pick mission
Build lists
Play mission
Update rosters
So your opportunity to deny playing comes before you actually see who is choosing the mission and what mission it will be. But a bad player could abuse the system by never agreeing to play while the other team has the mission pick. That will be something to try to prevent by good rules writing.