Is it because Vader was somehow 'good' in the end that the EU seems obsessed with making sure the villains are actually pretty good? No one seems actually villainous in the EU.
THRAWN- Really only wanted order and stability. Was motivated to protect the galaxy from the Vong. A hell of a guy in all regards. Frankly, the "heroes" were stupid for fighting him
TALON CARDE- Not only a honest and good smuggler who's kind to his employees, eventually he's not even a smuggler, but an 'information broker' who no doubt only deals with good guys.
DAALA- Sure she's a lunatic who wants superweapons to oppress the galaxy, but eventually she's President of the Galaxy, where she's downright benign and forces women's equality on the Empire.
MARA JADE- Pretty much a straight ahead hero after a bad start when she's semi-controlled by the dead Emporer.
DARTH VECTIVUS- A really nice guy who, despite being a Sith lord, spent all of his time in the honest pursuit of business ventures and spending time with his family, no doubt barbequeing with his kids.
LOST TRIBE OF THE SITH- A colony of Sith whose philosophy is to harness the Dark Side to help eachother out.
THE EMPIRE- By "Fate of the Jedi" the Moffs are still mainyl bad (the male ones at least) but the Empire is good, even Luke thinking it's just a great option for people who want a little more 'order' in their lives.
DARTH CAEDUS- Seemed evil, but only became a Sith lord when it was clearly laid out to him and the reader that things would be much much worse if he DIDN'T become a Sith Lord.
How are we supposed to root for the 'good guys' with this kind of stuff?!