The trick is that bad guys aren't 100% bad (and good guys aren't 100% good). Also, there's some cultural stuff, so their idea of "bad" may or may not map to yours.
And if you go past people to ideas, some ideas are pretty much universally bad in anime. For example, resurrection is only for evil people in anime; the good guys get reincarnated. Examples: Death Note, Mar Heaven, Shaman King, etc. If there's a counter-example, I've yet to see it.
Orochimaru & Kabuto's Kuchiyose: Edo Tensei ("Impure World Resurrection") technique, on the other hand is more the kind of "resurrection" I had in mind.
For example, at one point it argues that the typical plot complexity and subtlety in most anime is "extraordinary". I suppose this is true for something like Ghost in the Shell, Princess Mononoke, or some of the longer-running plot-driven manga, but that's a very biased sample. Perhaps that's a sign of the time in which the article was written -- in 2003, Americans' reference pool of anime was smaller, and so there was some pretty serious selection bias going on.