Exactly.
Also, you are asking the wrong question: it's either Enclave or the Unity, or The Master or Frank Horrigan.
In both cases, Fallout 1's antagonists win easily. The Enclave, as Languorous_Maiar stated, is way too "evil", and the normal player shouldn't ever want to join them (and even in that case, he couldn't). They're basically just dark techno-nazis.
The Unity, on the other hand, is much more subtle, and even if the player starts to fear them (and then fights them) early in the game, you eventually realize that they only look evil (but even then, it's a much more interesting evil than the Enclave's one), that they have feelings and faith in some goal that aims to bring peace to the wasteland (at the cost of necessary evils, like, killing the vault dwellers). The reason why you have the possibility to join the Unity is because you can actually believe in their choice and support it. However, even if you support it, by the end of the game you should have realized that you have to stop them anyway, not because they are evil, but because they made one mistake: the mutants are sterile, and thus their plan can't work at all. Your job is to make sure they realize that mistake or to stop them.
In the first Fallout game, you're fighting a perverted utopia. In Fallout 2, you're fighting a plain dystopia.