I decided to put Faction Commander into the mod. This will allow the player to choose weather they want to free play the faction war or do the story line. After you wake up at the beginning of the game, Lebedev asks you if you want to play the war or story line mode. If you choose faction war he gives you a choice of what faction you want to join then you are teleported to that factions base and you are given armor and weapons appropriate for your faction. The other factions have a command AI that works fairly well and there is an interface to command your own faction.
I have it integrated fairly well with what I already had in place. I still have to added armor for a few of the factions and give them all a unique twist. Like I want freedom suits to be quicker and lighter, but not has protective as the standard. Duty is the opposite. I'm not sure about the monolith suits yet, I'm trying to find some better models for them.
This does cause a few problems with the mechanics. I wanted each faction to have its own specialties like in the original game, but that just won't work out with the faction war since you won't be visiting rival bases. Also, I'm not sure if it broke the main story line again so I have to play through that again.
You've seen The Faction War, yes? It does pretty much exactly this which would make it a good base to build your Freeplay off of.
Yeah I've played the faction war. I really didn't want to do free play at all at first. But, the basic story can be beat in about 3 hours. Kinda of pointless to do all this work for just three or so hours of game play.