So many have been saying that the Enclave should die and there should be a "New Villain" The Enclave aren't the main Villain. They can still be around with a new Villain. And the Enclave aren't dead. We still don't know about Chicago and there are Vertibirds that leave the Broken Steel base so they could have gone into hiding to rebuild.
Enclave Vertibird leaving the Broken Steel Base (Proof)
So theres the Image of the Vertibird leaving the base at the end of Broken Steel. So there still out there as DC Remnants. And there could still be Enclave out in the East who knows? [EDIT]: So there were more than just one Vertibird that left. During the battle there were more air craft that left. And the Enclave are in other places too. Arcade Gannon states that the Enclave went to many different locations at the battle of Navarro so they spit up into groups of Remnants But there not dead.