Considering the fact that the planeteers where only a few steps away from eco-terrorists, I think that was the point. If the villians where actually more like the tropes they represented they would completely lose the family-friendly message and the series would end up looking like it supported terrorism.
Lutin Plunder was just a business man. Sure he was shady asshole, but still just a business man.
Hoggish Greedly was the same way. Hell, half time he was actually trying to help, but wasn't doing it in an eco-friendly way, so he got ass kicked.
Duke Nukem needed radiation to live.
Blight was the only villain on that show which could actually be considered a true villain.