I would disagree with this. The Enclave were just as much a threat in Fallout 2 as the Master's Army was in Fallout. Even more so, considering they had the capability to wipe out all mutant life, including the Super Mutants.
The Enclave were already wiped out in FO2, Bethesda bringing them back for FO3 was unimaginative and boring enough already (and they were wiped out once more

). To do that
again would just be sloppy. I'm not opposed to them making an apperance in NV (a small remnant force reduced to mercenaries for the highest bidder, or perhaps even a group that merely poses as the Enclave!), but never again do I want to see them as the main antagonistic faction. Enclave is done.
I'd like to see an apperance by the BoS as well, but not as the ridiculous knights in shining armor that they were in FO3. That completely deviated from the original purpose of the faction - to gather and preserve technology. So they'd overall be a neutral faction, not interested in what happens to wastelanders unless it directly interferes with their goals.
And about the Jedi/Sith comparison - whereas pretty much EVERYTHING (=major, future-shaping events and such, not some minor stuff) in the SW universe revolves around the Jedi and the Sith and their neverending conflict, imo that is not the case with BoS & Enclave in the Fallout universe.