If it's optional, then business as usual. If it's forced, I would be as bold to say Muse will put the nail in the coffin of competitive and clans. To quote dragonmere "But the setup of the lobby system and the balance of the game mechanics tends to heavily favor pick-up games, rather than organized play, and that seems to increase every patch. You're left with people competitively playing a casual game, rather than people casually playing a competitive game - like DOTA".
I hope Muse has the foresight to see it's the clans and competitive community keeping their game alive. Sure sales help bring in new players, but without friends made through your clan, player retention would be low. Player retention means we spread the word, we get more, keep players, they spread the word; Butterfly effect. If they make this game too frustrating to play as a group or clan, retention dies, game dies.
"Once a match is created, the blue and red sides will now have their win totals tracked." Based off of this, instead create a ranking system that is displayed in the lobby selection. A player can make an educated decision as to the difficulty of the lobby choices.
If this happens "Once a side attains a consecutive winning streak of 5, ship crews will swap places across blue and red team." We'll just all leave and create a new lobby. Sorry but, screw that system, I'm going to play with my friends.
