You'd be wrong on the Fallout 1 remarks or haven't you seen the "master wins" end movie? http://www.youtube.com/watch?v=PfyqlMBeQFU yeah it really looks like your helping out Vault 13 there. Fallout 2 was the only one with the concrete Kill the enclave save your village ending. Mostly because the Enclaves plan didn't give any outsiders options other then kill or be killed.
Ah, true, my bad, I did forget you could side with the Master. Consider that mostly revoked, although you are still forced to cooperate with Vault 13 right up until the end (much like the BoS in FO3). The FO2 point stands, though. Whether or not their plan precluded deviation from the proscribed main quest is irrelevant; Black Isle designed the faction and quests that way, and could easily have made the player able to side with the Enclave (or at least betray his village) and still continue with the game in some manner. They chose not to. That's a valid design choice, and there's nothing wrong with it, but it's kinda unfair to make excuses for FO2's linearity and accuse Fallout 3 of the same thing, especially when its main quest is less linear than FO2's.
But choosing to be Eden's agent of death made no sense. The Lone Wanderer had nothing to gain and everything to lose by doing so. What was his motivation? And the whole undercover agent thing was silly imo. It all just seemed forced and convoluted. The story clearly worked better if you chose the other path - the path you're apparently supposed to take which is also probobly in line with the canon. If it's not then the East Coast BoS no longer exists because they were whiped out by the Lone Wanderer.
I'm inclined to disagree that there was no sense behind helping Eden. The LW, as a vault dweller, would have believed himself to be non-mutated and so immune to the effects of the FEV. As such, it makes sense (from a certain perspective) to purge the wasteland of raiders, mutants and scavengers (that you didn't really like anyways) and clear the way for prime humans from the Enclave and the vaults to settle in a now-safe Capital Wasteland.
There's definitely a bit of shaky logic in there, sure, but it's definitely a defensible point of view.
Equally, one might ask, what might the Vault Dweller stand to gain from throwing his lot in with the Master and the Super Mutants? It's a non-canon choice based on some shaky logic that would destroy most of the factions we know and love today. Same principles, different decision. Siding with Eden or the Master is not the choice of a rational, sane, and good individual. Fortunately, the Vault Dweller and the Lone Wanderer don't have to be any of those things.