The hidden video at the end of KH final Mix was changed from another side another story to Deep dive. It showed much more of the organization and BHK passing someone who greatly resembled Riku. Throughout the video there was a countdown from the number 13. I think this means theres 13 members of the organization but I have no real evidence.
Its sensible to think that Riku and mickey would join the organization as the organization most commonly believed purpose is to study the heart from an unbiased view, no on the side of darkness or light. Just like Riku and at the end of reverse rebirth micky showed interest in Rikus method of accepting and controlling darkness and light.
Marluxia wanted to control darkness to overthrow the organization and Zexion wanted ot use Rikus darkness to counter act Marluxia so I wouldnt say the organization have any preference to either or.
When Vexen said he knew another side of Ansem I think he was referring to DiZ. I believe that DiZ is the leader of the organization and is also the body Ansem cast off. I think it will help if someone figures out what exactly DiZ stands for.