The Outcome agents had two of their chromosomes altered, giving them better recovery from physical injuries with additional unknown benefits. Since Treadstone agents were prone to physical and psychiatric ailments such as strength, speed, depression, anger, compulsive behaviors, headaches, sensitivity to light, and in Jason Bourne's case amnesia the program may have been designed to overcome those obstacles after Bourne went rogue and Treadstone was upgraded to Blackbriar.
A point of distinction between Outcome versus Treadstone or Blackbriar is that Outcome agents are better prepared to talk their way out of trouble rather than fight (cf. commentary on The Bourne Legacy deleted scenes).
When Bourne and Pamela Landy (Joan Allen) exposed both Treadstone and Blackbriar to the public in The Bourne Ultimatum film, Agent Byer (Edward Norton) decides to execute all of the Outcome agents worldwide and the R&D staff including Dr. Marta Shearing (Rachel Weisz).
Unlike Treadstone and Blackbriar, Opreation Outcome is not a CIA program. It is like the other two, in that it is a Beta program project.