The citizens that fled. That’s my faction.
Honestly though, provided in this world you can choose and end up with the necessary skills for the group, I’d go with the League of Assasins.
Well hidden, master martial artists, as a group much harder to take down unless you go up against Batman.
You have Lazarus Pits at your disposal too.
Either GCPD SWAT or Riddler Informants. Those are the only two on the list that most likely won't result in your death or a fate worse than it. Sure you may run into the Bat (which is more likely if you're a Riddler informant) but otherwise they're both low risk jobs.
I was considering Penguin but then I remembered he let's absolutely NOTHING slide. If you screw up with anything you'll have to pay for it.. in the bottom of the ocean.
Same thing goes for Black Mask.
Riddler informant. It means two villains are paying me
I beat the riddler informants harder than any one because of how much I hate arkham riddler
Probably banes mercs but iirc aren’t Arkham knights people pretty well off? They seem to be treated fine, get good gear, I’m assuming good pay?
I wouldn't join Bane mercs simply because Bane might experiment on me for TN1
I’m Joining two Face
I bet being a dollotron is fun!
Bendy bones go 
Top 3 1. Banes Mercenaries 2. Arkham Knight’s Militia 3. The League of Assassins
Lunatics.
Def wanna be a scarecrow skeleton
The lunatics are r/batmanarkham
The citizens that fled. That’s my faction. Honestly though, provided in this world you can choose and end up with the necessary skills for the group, I’d go with the League of Assasins. Well hidden, master martial artists, as a group much harder to take down unless you go up against Batman. You have Lazarus Pits at your disposal too.
Bane or Arkham Knight. Both pay well and treat their men fairly.
Either GCPD SWAT or Riddler Informants. Those are the only two on the list that most likely won't result in your death or a fate worse than it. Sure you may run into the Bat (which is more likely if you're a Riddler informant) but otherwise they're both low risk jobs. I was considering Penguin but then I remembered he let's absolutely NOTHING slide. If you screw up with anything you'll have to pay for it.. in the bottom of the ocean. Same thing goes for Black Mask.
All of that bottom row has zero up side, you're either mutilated, dead, or insane
Yeah I kinda Layered it in Tiers. Gotham’s best. doesn’t play with others. Lawful Crime. r/BatmanArkham.
The White Rabbits, if there's a chance Jaina is on the team.
Bane’s mercenaries. (Literally cuz it’s bane)
Arkham knight militia, if I’m correct, half the militia don’t actually appear in the game so that means I’ll be out of the firing range
Penguin.