MackieStingray: I'm uncertain of their plot synopsis for Fallout 2. Seems to me they said the plans of the Enclave were roughly the same as that of the Master, whereas I got the impression the Enclave wanted to kill everybody.
More philosophically, they tried to build a new America around their truths. Which means killing every post-apocalypse sociey which was labelled as "muties", while there were not mutants.
Master tried to found a society in which differences are avoided (whole mutants) because he believed differences among individuals are the only thing causes conflicts over centuries.