Yeah, DPS is a fairly useless stat. As is true in any form of "armor = damage reduction" system, slower more powerful attacks trump quicker but lighter attacks. The only reason to go with the quicker speeds is if you gain bonus damage or debuffs on a per-hit (or % per-hit) basis that makes up for the lost damage due to armor.

Compare to the pen-and-paper D&D 3.x system -- two-weapon fighting should technically have a high DPS, but it's almost always a suboptimal choice because a) it doesn't always apply and b) gets hosed in a hurry by any kind of significant damage reduction. The exception is if you manage to provide extra damage via something like Sneak Attack (I personally prefer Rogue 10+ with Crippling Strike and a pair of Wounding weapons to deal Strength and Constitution damage in addition to sneak attack damage; take the Savvy Rogue feat to apply the Strength damage at least to anything normally immune to Sneak Attack).