Cortana had a lot of time on her hands. After rewriting the suits firmware, reconfiguring the suits hardware, she decided to clone John and build each one their own suit.
Or she created an extra feature into John's suit that allowed it to project hardlight holograms capable of interacting with the environment and acting independent of the user.
When you think about it, she was active for 4 years. You think she just sat there staring longingly into John's. Visor. --- The future does not exist, because by the the time you're there it's already the present. Dr. Richard Epear - May 1st 2009