Found the answer and thanks for the reply....
Freedom is the "standard" way of playing. It allows you to create your character and start as either a Hero or a Villain.
The "Going Rogue" option allows you to create a character that starts in the parallel world of "Praetoria." You start as either a Loyalist or Resistance figher in Praetoria. From there, once you hit level 20, then can then decide to go to either the Rogue Isles (Villain) or Paragon City (Hero).