why not instead you have squads that choose a faction they are in. Keep the current squad system, but if you join a iceria or CTF map as a random and in the same faction as that squad in game, if you stay through the whole game, then you win personal faction points. These points you can use at your factions hide out to get more items unique to that faction, graalets, or ZC. You can increase your amount of faction points that you get throughout the game based on your preformance.
Bonus for joining and staying through whole game- 1 point
Win- 5 points
Kills- every 10 kills is 1 point
Bases captured- 2 points
Attacking bases (if you are near the base and killing defenders) 1 point
Defending Bases (if you are near the base and defending off attackers) 1 point