Master found the location of Vault 13 and dipped most of inhabitants - because of this he created strong and huge army of intelligent super mutants. What about the Brotherhood of Steel ? Would they be slaughtered by a mass of super muties or just they moved to east ?

I believe that Fallout 2 would focus on the war between Mutants and BoS.

You, as one of the last Normals, pick your side (likely with BoS) and fight the Mutants.
But don't forget Enclave, they would not submit to Mutants either. As easily the most technologically advanced faction they would win 1v1 against mutants but as Enclave manpower is low compared to Mutants, the war would have no winner.

As you, at end of FO2, would destroy mutant army, Fallout 3 would take place in a reviving human society, directed by Enclave. You would then "Fight The Power" or join the Enclave in the war for re-unification of USA. BoS would remain as an underground society, working with Enclave but there could be a war between them.

That's my theory..

Also rememebr that Mutants are sterile, there will be problems even if all available humans were 'dipped'. My idea would be that let Humans breed and take the children to be Mutants, thus eliminating the problem of mutant sterility.