The DPS numbers are misleading. First, the number only factors in basic attacks. Abilities aren't considered. In addition, abilities don't use the DPS number; they use the Damage number directly below the DPS number. Finally, DPS numbers factor in runes, but they assume that you are hitting the correct enemies. If your weapon has a rune that does extra damage to demons, but you're fighting humans, then your DPS isn't as high.
Now, pretty much every build relies on it's abilities to inflict the majority of it's damage. Auto attacks are only used as filler when abilities are on cooldown. As you get farther in the game, you get more abilities, and access to more sources of cooldown reduction, so auto attacks become a smaller portion of your damage output. Because of this, I would recommend focusing on weapons with higher Damage over weapons with higher DPS. Once you're looking at making a T3 weapon with T3 and T4 materials, then I would be okay with suggesting a weapon with higher DPS, but only because all T3 weapons would have the same Damage. If there was a difference in Damage, I'd suggest the one with higher Damage.