Here are the 5 ways I would do a New 52 version of the Freedom Fighters:
1. Continue to do a series of Mini-Series. Instead of a small link to each other, I would link the stories like Grant Morrison did with Seven Soldiers.
2. Make the 1st Arc like the "Brave New World" re introduction. Make a conspiracy the make like between the titles.
3. Use lesser characters from the old Quality Universe as a part of the first Arc. By doing this, you show readers that there is more to the old universe than the Freedom Fighters.
4.Actually use old Quality universe villains.
5. Connect them to the DC Universe.