I think I'm just gonna accept that every villain for Spidey films will be sympathetic. I don't know why they do this over, over, over, and over again. I mean, Lizard is the only villain that had damn reason to not be dark in some way. Norman is a rich *****ebag, Octavious is power hungry, Sandman is a hardened criminal, Brock is a dick.
Joker didn't have a good start.
Loki didn't have a good start.
Vanko didn't have a good start.
Zod didn't have a good start.
Red Skull didn't have a good start.
Sure, Joker wasn't empathetic, but he wasn't meant to be. His character was an archetype that was representative of larger thematic elements in the film (the ying to Batman's yang, etc...). Much of Nolan's series relied on literary cues like this. Which is great and works very well for that particular character in that particular story Nolan was telling...
Loki was very empathetic. You really felt for him, feeling angry and betrayed by his father, etc... He was the guy who had been dealt a bad hand and who lashed out.
Vanko is similar (although the character was really poorly written), a guy who goes out to avenge his father for reasons he believes to be true.
Zod was also very empathetic, an angry, misguided soldier doing his best to protect his people/lineage. He thought what he was doing was right.
Red Skull, well, yeah, he was pretty much just "evil" (and consequently, not that interesting).
So yeah, none of those characters are just out and out "evil", out to conquer the world or whatever (Except for the Skull. lol). Someone being a rich *****ebag, power hungry, hardened criminal or a dick are hardly interesting, multitiered characters that can bring forth some emotion or captivate the audience.