Blizzard isn't Blizzard North, and what's worse, Blizzard post-WoW isn't Blizzard of the 90s.
Diablo and D2 had bad guys. The monsters weren't sympathetic, we did not experience the story through from their perspective, and in fact when heroes from the prior game became villains they were fully corrupt; there are no shades of gray in Diablo. The evil exist to do terrible things then be vanquished.
Blizzard games didn't really have bad guys. Some of the characters were despicable monsters, but for at least some missions we either were those monsters, or at least we aided their cause. And I think that bleeds over into how Blizzard handles storytelling in Diablo 3. They want the villains to be characters, and they want us to hear from them, understand their motivations, get a sense of what makes them tick. I don't think that's a bad idea, except for my latter observation.
Post WoW Blizzard got soft. R rated content became PG-13. Metzen got old and had a couple kids and now everyone gets a redemption arc, and those who don't get redeemed are Cobra Commander types who bluster their way through defeat after defeat. It's like a morality play for the feel good generation. Everyone is OK, even the bad people, and the really bad people? They suck.
Reaper of Souls is a marked improvement story wise on everything Blizzard has released post WoW, so maybe good times are ahead.
I think its more the nature of the true 3d engine. It is much harder for them to get the appropriate dark colors in the engine they use. Instead, everything looks kind of cartoonish, ala WoW. It really loses the dark flavor that the 2d isometric engine was able to provide. I think it is much more of an issue of atmosphere rather than poor narrative.