Remember that a lot of the agents in Sentinel armor were guards at Camp X-Factor that seemed to be easily taken over by the brotherhood and if I remember right they were at the White House. I would suggest that they make a new prison somewhere for the captured mutants, since the destruction of the Triskellion probably let the prisoners there escape and make it somewhere more remote like an island. If you had a character like Gateway who could teleport the Sentinels to capture criminal mutants and teleport them back I think that would be cool. Maybe the warden could be Bastion, an officer from SHIELD and Nimrod could be an agent of SHIELD in high tech armor that could lead the Sentinels.