By the end of EP2, if there were a "civil war" among AMC agents, who do you think would be victorious? Research projects up to EP2 are available to fight but temporary weapons are discarded - every character would start with his/her full weaponry.
IMO, a melee fight would be more interesting. If this were the case, my bets are on Merlijn - who is supposed to be the strongest physical character (take a look at that devastating Dragonslayer) - or James, whose MJ12 injection makes his fists DYNAMITE!
The other scenario would be if every character had their "real" powers available during gameplay, which is their wiki description (power levels are nerfed in-game because, if not, there would be OP characters).
IMO, Micky would be victorious because of his perfect aim and intelligence.