Just look at the main quest for NCR, for example. The difference between them getting access to Vault 15 or not was large. If they managed to get access to it, they will be able to expand north and eastward, becoming a major power plus bring progress to almost the entire Core Religion. If they didn't, the Republic nearly collapsed. And remember, Vault 15 has already been gutted out years ago and doesn't even have their own GECK anymore, but it still made such a big difference.
My point is that the Enclave with all it's pre-war resources can easily resort law and order to large sections of America if they wanted to. Now that they have been defeated for 2 times in a role by the 'mutants', wouldn't the surviving members of their leadership think that 'You know, perhaps we should give up our plans for a final solution against the rest of the world and become a real government'?
In Fallout 2, if you have a high enough speech skill you can convince the Enclave Scientist that came up with the idea of the new FEV that it is wrong to commit genocide. Also, in Van Buren there were going to be survivors of the Enclave that decided to actually help rebuild America instead of focusing on killing all outsiders.
So do you think that the Enclave will be able to change their ways and become a somewhat benevolent dictatorship that resorts civilization (Similar to the New California Republic)? Or will they fight to the bitter end until every last one of their members either died, deserted, or surrendered?