Have you done their ending. Khans are just tribals like the 86 before and will have the same fate as them, the Boomers HOWEVER are in Caesar's eyes to powerful to attack and he leaves them alone - if you complete "Volare!" and get them the bomber.
The Enclave are also left to go on their way if Caesar is alive and they ally, he knows their power far surpasses his own.
The Khans are taken into the Legion "Though many Great Khans mourned the death of their tribe,
many more were ultimately satisfied with their revenge against NCR." Of the fit people to join the Legion that doesn't sound that bad if they were happy.
Caesar is mericful to some, FotA for example are given safe passage out of the Mojave out of his respect for them and his past. They watch over most towns
peacefully, not imposing heavy taxes like NCR.